Using the MegaSquirt-I (MSnS-E) with the Honda ignition module

This is a straightforward option with a V3.0 or V3.57 board.

MegaSquirt-I PCBv3.0 Mods Required: 

• Build the VR conditioner circuit, as described in Step 51 of the MegaManual. All our preassembled Megasquirts with the V3.0 board come with this circuit installed.
• Jumper TachSelect to VRIN.
• Jumper TSEL to VROUTINV.
• You may need to adjust the VR trim pots, R52 and R56, when this is installed on a running engine.  A usual base setting is to turn them all the way counterclockwise.
• Run a jumper wire from the negative leg of D14 to IGN.

That's it!

MegaSquirt-I PCBv3.57 Mods Required: 

• Put the JP1 jumper in the 1-2 position and J1 in the 5-6 position.
• You may need to adjust the VR trim pots, R52 and R56, when this is installed on a running engine.  A usual base setting is to turn them all the way counterclockwise. Note that the trim pots on these boards do not click - giving them 5 counterclockwise turns will make sure they have been turned far enough.
• Run a jumper wire from PAD1 to the center hole of the Q16 slot.
• Remove R58.

That's it!

External Ignition Wiring

• Wire the TDC positive signal to pin 24 on the Megasquirt, and ground the negative wire from this sensor. On our preassembled wiring harness, you can use the shield on the IGN wire as a ground.
• Wire the Honda ignition module input to pin 36 on the Megasquirt.

MSnS-E Ignition Configuration

• Configured for MSnS Spark Output using LED 17.
• In MegaTune, you MUST set Spark Output Inverted to Yes. 
• For dwell settings, start with a running dwell of 3.0 and a cranking dwell of 4.0.
• The Trigger Angle setting will depend on the physical location of the trigger pickup. Often, an angle of 10 degrees will work. To set the timing with MSnS-E, go to the Spark Settings menu and set Fixed Angle to 10 degrees. You can then set the ignition timing to 10 degrees with the engine running, using a timing light (Note: Some Honda engines have a red mark for purposes of setting base timing along with a white mark at TDC. Check your service manual to see exactly where your timing marks are located. If it is at another angle like 16 degrees, you can set the fixed angle to that angle and line up the red mark). Once you have set the base timing, set Fixed Angle to -10. This will tell MSnS-E to use the timing map.

Using the MegaSquirt-I (MSnS-E) with a 7 Pin HEI module

If you happen to have a V2.2 board, using a HEI module can be easier than building a VR conditioner input circuit on a board that never had one.  The MSnS-E Manual has detailed information about how to set up Megasquirt to work with an HEI ignition. This write-up uses slightly different pins.

MegaSquirt-I PCBv2.2 Mods Required: 

• The input mods are to invert the input signal from the HEI module's tach signal.  The HEI module will ground pin 24 to trigger a spark input.
• Remove D5, D8, and R10.
• Replace D8 with a 1.3 k resistor. You may substitute a resistor between 1.3 k and 2.0 k.
• Remove the jumper from XG1-XG2. Jumper XG1 to the right (non-banded) side of D5.
• Solder a jumper from the lower hole where R10 used to be (the hole nearest U4) to the upper lead of R11. This will provide a 5 volt pull-up.
• You will use LED 17 and LED 19 as outputs.
• Solder a 1 k resistor from the negative lead of D17 (it's marked with a small - sign) to the right lead of R23 to provide a 5 volt pull-up on the output.
• Run a wire from the negative terminal of D17 to jumper X12.
• Now you will add the equivalent mod to D19.
• Solder a 1 k resistor from the negative lead of D19 to the right lead of R27.
• Run a wire from the negative terminal of D19 to jumper X11.
• That's it!

External Ignition Wiring

• For this one, you'll remove the stock Honda ignitor outright.
• Connect the positive terminal of the coil to the stock coil wire and to the + pin on the HEI module.
• Connect the negative terminal of the coil to the C pin on the HEI module.
• Wire the distributor's VR sensor to the HEI module VR inputs.
• The R pin is the HEI module's tach output. Connect it to pin 24 on the Megasquirt, or the Tach pin on the relay board. Note that the DIY Autotune wiring harness has a shielded wire - connect only the inner wire to this pin!
• Connect the E pin to pin 27.
• Connect the B pin to pin 25.

MSnS-E Ignition Configuration

• Under Codebase and Output Functions, set HEI Ignition to "GM 7pin HEI" and the other options to Off.
• Set LED 17 function to Spark Output A, and LED 19 function to Spark Output B.
• In Spark Settings, set the Trigger Angle to 10 degrees and set Spark Output Inverted to No.
• To set the timing with MSnS-E, go to the Spark Settings menu and set Fixed Angle to 10 degrees. You can then set the ignition timing to 10 degrees with the engine running, using a timing light. Once you have set the base timing, set Fixed Angle to -10. This will tell MSnS-E to use the timing map.
• Under dwell settings, set dwell control to fixed duty and the spark output duty cycle to "Minimal for HEI4."

Using the MegaSquirt-II PCBv3 with the Honda ignition module

MegaSquirt-II PCBv3.0 Mods Required: 

• Build the VR conditioner circuit, as described in Step 51 of the MegaManual. All our preassembled Megasquirts with the V3.0 board come with this circuit installed.
• Jumper TachSelect to VRIN.
• Jumper TSEL to VROUTINV.
• You may need to adjust the VR trim pots, R52 and R56, when this is installed on a running engine.  A usual base setting is to turn them all the way counterclockwise.
• Jumper JS10 to IGBTIN and IGBTOUT to IGN.
• Install a TIP120 or similar switching transistor in the Q16 slot. You will not be using this to drive the coil directly so you do not need a transistor meant for serving as an ignition module, although an ignition transistor like a BIP373 will work too.

That's it!

MegaSquirt-II PCBv3.57 Mods Required: 

• Put the JP1 jumper in the 1-2 position and J1 in the 5-6 position.
• You may need to adjust the VR trim pots, R52 and R56, when this is installed on a running engine.  A usual base setting is to turn them all the way counterclockwise. Note that the trim pots on these boards do not click - giving them 5 counterclockwise turns will make sure they have been turned far enough.
• Jumper JS10 to IGBTIN.
• Install a TIP120 or similar switching transistor in the Q16 slot. You will not be using this to drive the coil directly so you do not need a transistor meant for serving as an ignition module, although an ignition transistor like a BIP373 will work too.

That's it!

External Ignition Wiring

• Wire the TDC positive signal to pin 24 on the Megasquirt, and ground the negative wire from this sensor. On our preassembled wiring harness, you can use the shield on the IGN wire as a ground.
• Wire the Honda ignition module input to pin 36 on the Megasquirt.

Megatune Ignition Configuration:

• Trigger offset = 10° (this will vary, depending on the distributor orientation, see notes at the end of the article)
• Ignition Input Capture to 'Falling Edge'
• Cranking Trigger to 'Trigger Rise'
• Coil Charging Scheme to 'Standard Coil Charging'
• Spark Output to 'Going High (Inverted)'

Set the dwell to 3.0 ms.

More information on setting Trigger Offset:

You must also set the initial position of the trigger (called the 'trigger offset'), then check it using the Trigger Wizard in MegaTune  (Tools Menu).  The trigger offset setting will vary according to your distributor position (where it is in rotation) but you'll need to set it properly...  Basically you use the Trigger Wizard and adjust the 'trigger offset' and/or twist your distributor until the advance number in the Trigger Wizard matches what you're reading with your timing light.  The +/- buttons on the trigger wizard will adjust your trigger offset.  You'll need to use these buttons and a timing light to make the number on your light, and the big number on the left in the Trigger Wizard, match up.

Here's the information on this direct from the MegaTune Manual:

Before tuning your advance table, be sure to use a timing light to verify that your 'trigger offset' is calibrated. Changing the Trigger Offset in MegaTune will not change the displayed advance, instead, it changes the actual advance as seen with a timing light. Your goal is to make these two match.

To do this, get your engine warmed-up (otherwise the timing moves as the temperature increases) and idling, then use a timing light to verify to be certain your actual advance as shown by a timing light equals your the advance display on the advance gauge in MegaTune. (8° in this case). (Note that positive numbers denote BTDC, and negative numbers denote after TDC.)

Image courtesy of Bowling and Grippo