How to MegaSquirt Your Foxbody Mustang 5.0

MSPNP ALERT!

Plug-N-Play Options

These are fully loaded plug and play standalone ECUs with plenty of extra inputs and outputs to get the job done right allowing you to datalog and control just about anything you need.  With a 4 bar MAP sensor built in for massive boost levels, output for an electronic boost control valve, nitrous control, and a stack of other features.  This will get ‘er done!

Standard Features:

  • Full control of your fuel and ignition tables
  • Launch control aka 2-step
  • Flat shift/no lift shifting
  • Flex Fuel/E85 Support with added flex fuel sensor
  • Electronic Boost Control (requires boost solenoid, but they’re cheap)
  • Allows use of a wideband oxygen controller/sensor to real time fueling corrections
  • Table switching- Change the fuel and spark maps on the fly with a switch
  • Safeties like Overboost Protection can save the day if you turn the boost up too high
  • Real time barometric correction
    Lots more….
    The MSPNP Gen2 ECU comes with the TunerStudio Tuning software, a base map for a lightly modified 5.0 to use as a startup map, and tuning cable.  These are our most powerful production plug and play systems for Fox Body Mustangs (and SN95 Mustangs) yet!

MS3Pro PNP Additional Features:

  • Higher resolution tables for fuel and ignition
  • Sequential Fuel Injection
  • Optional Sequential Ignition (aka Coil On Plug or Coil Per Plug) capabilities for insane ignition system energy potential
  • Onboard datalogging to an SD Card inside the ECU, allowing for easy download of log files onto your laptop across the USB/Tune Cable
  • Every major feature from launch, idle, knock control through nitrous, turbo boost control, etc are refined and improved
  • Additional Engine Safeties and Shutdowns– get a warning light, or just shut down the party, if something starts to go awry.  Too much boost?  Temps too high?  AFR too lean?  Give yourself a warning– or shut it down automatically and save the day!

MegaSquirt your Fox Body and SN95 Mustang

Keep reading below for how to install our DIY kit type MegaSquirt ECUs in your Fox Body or SN95 Mustang GT or LX.  This gets technical fast and isn’t plug-and-play at all, but we can help you make it happen!  For easy installation allowing you to be up and running in minutes ready to tune, make sure to check out our MSPNP ECUs for these cars!  

86-95 SN95 and Fox Body Mustang 5.0 Ignition Notes

These cars have TFI modules on the distributor (86-93) or remotely mounted (94-95).  You can do these using the PIP wire on the TFI distributor as the tach input to MegaSquirt-I running MSnS-E firmware, or a MegaSquirt-II running the standard MS2 firmware.  More information on each implementation and any modifications required are below.

86-93 5.0l Foxbody Mustangs  (GT and LX)

On all of these Mustangs, Megasquirt allows you to completely remove the EEC-IV ECU and replace it with the MegaSquirt. The MegaSquirt can take over all of the functions except some of the emissions control devices.

Basically you get the TACH input to the MegaSquirt (pin 24) from the PIP signal on the TFI module, and you send the outgoing MS ignition signal back out from pin 36 to the SPOUT pin on the TFI module.  You can use the Megasquirt to control the TFI module, which is quite straightforward. Or if you want to give your system the ability to cut the fuel, you can control an MSD box or the coil directly, bypassing the TFI module on the output side.

94-95 5.0l SN95 Mustangs

On 1994-1995 Ford Mustang GT or LX cars (SN95), you can use the MegaSquirt to remove the stock ECU if you have a manual tranmsission. You only need to keep the stock ECU if you are running an automatic, since MegaSquirt  does not have transmission control outputs. Alternatively, you can use a MegaSquirt to control the engine and a MicroSquirt or GPIO board to control the transmission.

Based on a remote mount TFI Module and a separate distributor.  Same story as the 87-93 for the most part, you just get the return the signals to different places.  Basically you get the TACH input to the MegaSquirt (pin 24) from the PIP signal on the TFI module, and you send the outgoing MS ignition signal back out from pin 36 to the SPOUT pin on the TFI module.

Thanks to ‘MegaScott’ on the MSEFI forums for this drawing and permission to use it here

Almost any MS variant can be used on these cars with full fuel and ignition control. The MS2 adds more precise fuel and timing control with a faster processor, while MS3 opens up even more options, including full sequential EFI with the stock distributor.

Using the MegaSquirt-II PCBv3 with the factory TFI Ignition

If you’re assembling your MegaSquirt-II from a kit (Part# MS230-K):

  • For the most part, stick with the standard assembly documentation.  We’ll cover any differentiation from that doc here.
  • Step 22:  You really don’t need any of the 5 jumper wires listed in this step.  If you ever use this ECU on a different car that does use a stepper motor IAC you can add them then.  Personally, I’d leave them out for your Mustang as you can use the IAC outputs for other cool stuff later.
  • Step 50:  You’ll be installing the ‘Hall/Optical Input Circuit’  (currently all steps under 50a).  If you see any steps that say ‘only do this if you are triggering from the negative terminal of the coil’, you aren’t, so don’t. 😉
    • INSTEAD OF JUMPERING D2 as directed here, install a 1k 1/4watt resistor in it’s place.
  • Step 51:  You don’t need these components, but I’d recommend installing them anyways in case the MS ECU is ever used on another car with a VR sensor.
  • Step 52:  Set the jumpers for Hall/Optical/Points.  That would be XG1 to XG2, OPTOIN to TACHSELECT, and TSEL toOPTOOUT.
  • Step 59:  You will be doing the PWM Idle Mod using the parts from the mk-PWMIAC.  That means you leave D8 out when you get to this step.
  • Step 62:  Follow the steps in the blue box following step 62 to finish installing the mk-PWMIAC for control of your 2-wire idle valve.
  • Step 65:  You ARE USING THE IGBT High Current Ignition Driver Circuit (MK-BIP373 or other switching transistor required).  That means you complete step 65.  Install everything just as this step directs you to (which does mean no R57), and install the jumpers to enable the circuit. (IGBTIN to JS10 and IGBTOUTto IGN) Note that if you are using a metal backed transistor like a BIP373 or certain switching transistors, you must use a mica insulator under Q16.

NOTE– there was originally an error in the MS2 TFI docs that said to leave R43 out for this setup, I’ve found that to be incorrect and it’s been corrected it in the MS2 docs, so LEAVE R43 in!

  • Step 69:  Choice time — Install the PWM Flyback Circuit bits….
  • Step 71:  Choice time — Install the  current limit circuit for FET protection….
  • Step 74:  Do not install Q20 (part of the mk-PWMIAC mod)
  • Step 75:  Leave R39 out and jumper it instead (part of the mk-PWMIAC mod)
  • Now for the final step (Mod for TFI Ignition Output).  Use a 100ohm, 1/4watt resistor.  Solder one leg of this to the IGN/IGBTOUT jumper wire.  Solder the other leg of this to the hole labeled S12.  (Not to be confused with the hole labeled S12C !)  The S12 label is on TOP of the board, but you’ll place this resistor on the bottom generally.  Check out this diagram.

That’s it– you’ve got your Megasquirt-II Engine Management System fully prepared to receive the ignition input from your TFI module, and return the Megasquirt controlled ignition output back to the TFI module giving you full control of your stock TFI ignition system.  At the same time you’ve also ‘modded’ the FIDLE output to be able to handle your Pulse-Width Modulated (PWM) Idle-Air-Controller (IAC). 

If you’re modifying a DIYAutoTune.com MS2357-C MegaSquirt-II Assembled ECU:

Input Mod:

  • Jumper J1 to the 3-4 position and JP1 to the 1-2 position.

Output Mod:

  • There will be a jumper wire from JS10 over to the center hole of Q16.  Desolder and remove this (don’t just cut it, you’ll need the holes clear of solder).
  • Rewire this jumper so it goes from JS10 to IGBTIN.
  • Install a BIP373 with mica insulator in the Q16 slot.
  • Use a 100ohm, 1/4watt resistor.  Solder one leg of this to the center hole of Q16.  Solder the other leg of this to the hole labeled S12.  (Not to be confused with the hole labeled S12C !)  The S12 label is on TOP of the board, but you’ll place this resistor on the bottom generally.

V3.57s do not need to be modified for IAC output.

Fox Body and SN95 Mustangs – Wiring it all up…

I couldn’t possibly hope to cover all of the wiring information that is so thoroughly covered in the MSExtra Manuals here, and for the most part there’s really no need to.  Sensors and Injectors wire up the same on most every vehicle out there… You can use MSExtra’s schematic & wiring section for this information.  I’m going to cover the Mustang specific stuff here…. that would be the Ignition Wiring and the PWM IAC valve wiring.  Those are the only two missing pieces of the puzzle.

Ignition Wiring:

  • Input: Pin 24 on MS-II DB37, PIP from TFI module
  • Output: Pin 36 on MS-II DB37, SPOUT to TFI module

Image courtesy of Bowling and Grippo

PWM IAC Wiring:

To wire this up without the relay board (directly to the ECU), wire up the hot wire from the idle valve to switched 12v+ (hot in RUN), and wire the negative wire from the idle valve directly to pin 30 on the MegaSquirt DB37.

To wire this up with the relay board, you will need to jumper the FIDLE relay to take it out of the loop, below is a picture of how to do this. Then you will still wire up the hot wire from the idle valve to switched 12v+ (you could use the fuel pump power from the relay board), and wire the negative wire from the idle valve directly to the FIDLE terminal on the relay board. This will allow full control of your PWM idle valve.

Image ‘borrowed’ from the MSnS-E pages

You should also put a 1N4001 diode across the PWM Idle valve itself – the banded end goes to the 12 Volt supply, the non-banded end goes to the lead that goes to MegaSquirt (this diode is for flyback purposes on the idle valve).

TunerStudio Ignition Configuration for MS2/Extra:

  • Spark Mode to “Basic Trigger“
  • Trigger Angle / Offset should be set at 10 degrees to start. Adjust as needed to make the timing you see with a timing light match the timing in TunerStudio.
  • Ignition Input Capture to ‘Falling Edge‘
  • Spark Output to ‘Going High (inverted)‘
  • Number of Coils to Single Coil
  • Spark A Output Pin  to JS10
  • Dwell type to Fixed Duty
  • Dwell duty to 50%

IAC settings for closed loop can be found in the base map below.

Coolant (CLT) / Intake (IAT/MAT) Temperature Sensor Calibration

You can use your stock IAT and CLT sensors, and with the MegaSquirt-II you can calibrate these sensors through TunerStudio.  It’s best to leave the standard R4 and R7 ‘Bias Resistors’ in place in the MegaSquirt and just configure this in the software.  You get better accuracy this way.

  • Open TunerStudio>Tools>Calibrate Thermistor Tables
  • Select ‘Coolant Temp Sensor’, Select ‘Fahrenheit’, and enter these values:
  • Click OK and the Coolant sensor will be calibrated.
  • You’re not quite finished yet though— You need to repeat these steps, but choose ‘Air Temperature’ as the sensor table and use the same temp and resistance values from above as the sensors use the same curve.  This will calibrate the IAT as well.

NOTE– Make sure you chose Fahrenheit or your readings will be WAY off with the above values….


Using the MegaSquirt-II PCBv3 with a MSD 6A Ignition Box on a TFI Vehicle

If you’re assembling your MegaSquirt-II from a kit (Part# MS230-K):

  • For the most part, stick with the standard assembly documentation at MSExtra.com.  I’ll just be covering any differentiation from that doc here.
  • Step 22:  You really don’t need any of the 5 jumper wires listed in this step.  If you ever use this ECU on a different car that does use a stepper motor IAC you can add them then.  Personally, I’d leave them out for your Mustang as you can use the IAC outputs for other cool stuff later.
  • Step 50:  You’ll be installing the ‘Hall/Optical Input Circuit’  (currently all steps under 50a).  If you see any steps that say ‘only do this if you are triggering from the negative terminal of the coil’, you aren’t, so don’t. 😉
    • INSTEAD OF JUMPERING D2 as directed here, install a 1k 1/4watt resistor in it’s place.
  • Step 51:  You don’t need these components, but I’d recommend installing them anyways in case the MS ECU is ever used on another car with a VR sensor.
  • Step 52:  Set the jumpers for Hall/Optical/Points.  That would be XG1 to XG2, OPTOIN to TACHSELECT, and TSEL toOPTOOUT.
  • Step 59:  You will be doing the PWM Idle Mod using the parts from the mk-PWMIAC.  That means you leave D8 out when you get to this step.
  • Step 62:  Follow the steps in the blue box following step 62 to finish installing the mk-PWMIAC for control of your 2-wire idle valve.
  • Step 65:  You ARE USING THE IGBT High Current Ignition Driver Circuit (MK-BIP373 required).  That means you complete step 65.  Install everything just as this step directs you to (which does mean no R57), and install the jumpers to enable the circuit. (IGBTIN to JS10 and IGBTOUTto IGN) Note that if using a metal backed transistor like a BIP373, you must use a mica insulator under Q16.

NOTE– there was originally an error in the MS2 TFI docs that said to leave R43 out for this setup, I’ve found that to be incorrect and it’s been corrected it in the MS2 docs, so LEAVE R43 in!

  • Step 69:  Choice time — Install the PWM Flyback Circuit bits….
  • Step 71:  Choice time — Install the  current limit circuit for FET protection….
  • Step 74:  Do not install Q20 (part of the mk-PWMIAC mod)
  • Step 75:  Leave R39 out and jumper it instead (part of the mk-PWMIAC mod)

That’s it– you’ve got your Megasquirt-II Engine Management System fully prepared to receive the ignition input from your TFI module, and return the Megasquirt controlled ignition output out to your MSD 6a CD Ignition box– Giving you full control of your fuel and ignition!.  At the same time you’ve also ‘modded’ the FIDLE output to be able to handle your Pulse-Width Modulated (PWM) Idle-Air-Controller (IAC). 

If you’re Modifying a DIYAutoTune.com MS230-C MegaSquirt-II Assembled ECU:

Input Mod:

  • There will be a jumper wire in the D2 position.  Remove this jumper wire and place a 1k 1/4 watt resistor in this position instead.

Output Mod:

  • There will be a jumper wire from JS10 over to IGN.  Desolder and remove this (don’t just cut it, you’ll need the holes clear of solder).
  • Install new jumper wires to enable the IGBT High Current Ignition Driver Circuit (IGBTIN to JS10 and IGBTOUT to IGN)

That’s it– you’ve got your Megasquirt-II Engine Management System fully prepared to receive the ignition input from your TFI module, and return the Megasquirt controlled ignition output out to your MSD 6a CD Ignition box– Giving you full control of your fuel and ignition!.  At the same time you’ve also ‘modded’ the FIDLE output to be able to handle your Pulse-Width Modulated (PWM) Idle-Air-Controller (IAC).

If you’re modifying a DIYAutoTune.com MS2357-C MegaSquirt-II Assembled ECU:

Input Mod:

  • Jumper J1 to the 3-4 position and JP1 to the 1-2 position.

Output Mod:

  • There will be a jumper wire from JS10 over to the center hole of Q16.  Desolder and remove this (don’t just cut it, you’ll need the holes clear of solder).
  • Rewire this jumper so it goes from JS10 to IGBTIN.
  • Install a BIP373 with mica insulator in the Q16 slot.

V3.57s do not need to be modified for IAC output.

Wiring it all up…

I couldn’t possibly hope to cover all of the wiring information that is so thoroughly covered in the MSExtra Manuals here, and for the most part there’s really no need to.  Sensors and Injectors wire up the same on most every vehicle out there… You can use the MSExtra’s schematics & wiring section for this information.  I’m going to cover the Mustang specific stuff here…. that would be the Ignition Wiring and the PWM IAC valve wiring.  Those are the only two missing pieces of the puzzle.

Ignition Wiring:

  • Input: Pin 24 on MS-II DB37, PIP from TFI module
  • Output: Pin 36 on MS-II DB37, connected to white wire (points trigger) on the MSD 6a box

Image courtesy of Bowling and Grippo

PWM IAC Wiring:

To wire this up without the relay board (directly to the ECU), wire up the hot wire from the idle valve to switched 12v+ (hot in RUN), and wire the negative wire from the idle valve directly to pin 30 on the MegaSquirt DB37.

To wire this up with the relay board, you will need to jumper the FIDLE relay to take it out of the loop, below is a picture of how to do this. Then you will still wire up the hot wire from the idle valve to switched 12v+ (you could use the fuel pump power from the relay board), and wire the negative wire from the idle valve directly to the FIDLE terminal on the relay board. This will allow full control of your PWM idle valve.

Image courtesy of MSExtra.com

You should also put a 1N4001 diode across the PWM Idle valve itself – the banded end goes to the 12 Volt supply, the non-banded end goes to the lead that goes to MegaSquirt (this diode is for flyback purposes on the idle valve).

TunerStudio Ignition Configuration for MS2/Extra:

  • Spark Mode to “Basic Trigger“
  • Trigger Angle / Offset should be set at 10 degrees to start. Adjust as needed to make the timing you see with a timing light match the timing in TunerStudio.
  • Ignition Input Capture to ‘Falling Edge‘
  • Spark Output to ‘Going High (inverted)‘
  • Number of Coils to Single Coil
  • Spark A Output Pin  to JS10
  • Dwell type to Fixed Duty
  • Dwell duty to 50%

IAC settings for closed loop can be found in the base map below.

Coolant (CLT) / Intake (IAT/MAT) Temperature Sensor Calibration

You can use your stock IAT and CLT sensors, and with the MegaSquirt-II you can calibrate these sensors through TunerStudio.  It’s best to leave the standard R4 and R7 ‘Bias Resistors’ in place in the MegaSquirt and just configure this in the software.  You get better accuracy this way.

  • Open TunerStudio>Tools>Calibrate Thermistor Tables
  • Select ‘Coolant Temp Sensor’, Select ‘Fahrenheit’, and enter these values
  • Click OK and the Coolant sensor will be calibrated.
  • You’re not quite finished yet though— You need to repeat these steps, but choose ‘Air Temperature’ as the sensor table and use the same temp and resistance values from above as the sensors use the same curve.  This will calibrate the IAT as well.

NOTE– Make sure you chose Fahrenheit or your readings will be WAY off with the above values….

Using the MegaSquirt-III and MS3X

Note – if you’re not using an MS3X, use the MS2 directions.

Hardware setup

  • Follow the standard build guides for MS3, including TachSelect to VRIN and TSEL to VROUT on a V3.0 board. (On a V3.57 board, put main board jumper JP1 in the 1-2 position, and J1 in the 3-4 position).
  • Make sure you have the pull up jumper for 12 volt tach output (JP3 on the MS3X) is across both JP3 pins.

Wiring it all up…

I couldn’t possibly hope to cover all of the wiring information that is so thoroughly covered in the MSExtra Manuals here, and for the most part there’s really no need to.  Sensors and Injectors wire up the same on most every vehicle out there… With an MS3, use the wiring diagram in the MS3 manual. I’m going to cover the Mustang specific stuff here…. that would be the Ignition Wiring and the PWM IAC valve wiring.  Those are the only two missing pieces of the puzzle.

Ignition Wiring:

  • Input: Pin 24 on main board DB37, PIP from TFI module
  • Output: Pin 26 on MS3X DB37, connected to SPOUT on distributor. Can also be wired to the white wire of an MSD6 box.

PWM IAC Wiring:

To wire this up without the relay board (directly to the ECU), wire up the hot wire from the idle valve to switched 12v+ (hot in RUN), and wire the negative wire from the idle valve directly to pin 9 on the MS3X DB37.  This uses the PWM idle driver on the MS3X board.

To use signature PIP mode for sequential injection, you need V1.1 or later code.

TunerStudio Settings:

  • Spark Mode to “Basic Trigger“
  • Ford TFI Options to “TFI Signature PIP“
  • Trigger Angle / Offset should be set at 10 degrees to start. Adjust as needed to make the timing you see with a timing light match the timing in TunerStudio.
  • Ignition Input Capture to ‘Falling Edge‘
  • Spark Output to ‘Going High (inverted)‘
  • Number of Coils to Single Coil
  • Spark Hardware in use to Tacho
  • Dwell type to Fixed Duty
  • Dwell duty to 50%

More Information

Looking for a base map?

We’ve now posted a Mustang Base Map for you to download, for MS2/Extra 2.1.0 firmware. Here is a brief rundown of the specs on the test car. This map should be a good starting point for a mildly modified car.

  • 1993 5.0 Mustang GT
    • Stock short block
    • Stock 19 lb/hr injectors
    • GT40P (Explorer) head swap
    • Edelbrock intake manifold
    • Professional Products throttle body
    • Shorty headers
    • Flowmaster exhaust

Other Things the ECU Controls

The stock ECU controls a couple other devices in these cars besides the injectors, ignition, and IAC valve, but not very much. Here’s what to do about the ones you will need to control.

Fuel pump: This is a standard output on the Megasquirt. Wire the Megasquirt pin 37 to the fuel pump relay wire that went to the stock ECU.

Cooling fans: The ’94-’95 SN95 Mustangs generally had two cooling fan control outputs, one for low speed and one for high speed. Use one MK-RelayCtrl mod kit for each of them if you want to control the fans with MS1. See below for a picture of an installed relay control mod kit.

If you have an MS2, you can use the two stepper IAC outputs to drive the relays – just wire the two IAC1 wires across the coil of the low speed fan relay, and the IAC2 wires across the coil of the high speed fan relay. The ECU did not control the fans on ’93 and earlier models.

Air conditioning: The ECU can turn the A/C off at full throttle, but it does not turn the A/C on. You can use an MK-RelayCtrl if you want to add this function, but the A/C can operate on its own with no intervention from the ECU. It just won’t shut off at full throttle.


The gauges and air bags on these cars don’t connect to the Fox Body Mustang’s ECU, so you won’t need to worry about them. The tachometer is driven off the TFI ignition module, so once you control the TFI module the tach will follow along. The other gauges connect to their own sending units.

The stock intake air temperature sensor threads into the intake manifold, where it can absorb heat through the walls of the manifold which can sometimes cause heat soak after a hot shutdown if you attempt to restart soon after.  You can compensate for that in your tuning, but it will require more tuning work and know how, and it’s simpler for most to move it somewhere it won’t heatsoak so much in the first place. Moving it to the intake plumbing upstream of the throttle body (but, on a turbo car, downstream of the intercooler) can give a more accurate reading without the extreme heatsoak concerns.

Suggested parts

You can use either a Megasquirt I, II or III on these cars, depending on your budget. You will be able to use your existing sensors except for the MAP sensor which is built into the MegaSquirt.

ECU options:

Mod kits discussed in this article:

  • MK-BIP373 is required for many of the mod versions.
  • MK-RelayCtrl will give you a relay control output if you are using an MS1 on a ’94-’95 car, or want to control the AC cutout relay.
  • MK-PWMIAC for idle control
  • MK-Pullup will provide the pullup resistor needed for the internal mods described above

Other recommended parts