LS motors: Dealing with the stock ECU’s other functions

On many LS powered cars, the factory engine control unit does a lot more than controlling the engine. In many cases, if you’re putting MegaSquirt on a car that came with an LS motor, we recommend installing the MegaSquirt in parallel with the stock ECU if you want these features to keep operating. If the LS motor is being swapped into an older chassis, you’ll need to find a way to replicate these features using the MegaSquirt, and possibly additional hardware. Here’s what the LS ECUs (and some modules they interface with) control, and what you can do about them.

Air conditioning

The MS3 has a dedicated A/C control option. The MS2 has this in the works for the 3.3 version of MS2/Extra (in beta development at the time of this writing). Alternatively, you can control the A/C with a relay tied to the A/C switch and pressure switch, like on a carbureted car, and not wire the A/C to the MegaSquirt at all.


The only known factory LS application where the stock ECU doesn’t connect to the alternator is the ’98-’02 F-body. However, most of the “computer controlled” alternators on these engines can be placed in an automatic mode by wiring their “L” terminal to the dashboard alternator warning light (which would get switched 12 volt power if your car originally did not have one).  When the L terminal is connected to a lamp, the alternator will power up and put out charging voltage. This trick works on any alternator with a four terminal connector where the terminals are marked P, L, F (or F and I on the same terminal), and S. The remaining three terminals are left disconnected.

Automatic transmission

If you’ve simply put a TH350 or other mechanical transmission behind the motor, this is a non-issue. MS3 also has an output feature for lock up torque converters. But if you’re running a 4L60E or 4L80E, you’ll need an external control box. Two available options are theMegaShift and James Murray’s MicroSquirt transmission control code. These tie in with the MegaSquirt over the CAN bus. You can also use other off the shelf aftermarket transmission control units, although they aren’t quite as closely integrated.

Cooling fans

If your motor isn’t set up for an engine driven fan (or you want to remove the fan and run an electric fan), it’s easy to set up the MS for fan control. With the MS3-Pro or MS3X, just use an unused PWM, medium current, or high current output to run a fan relay. For MS2, see how to add a relay control circuit.

Electronic throttle control

Currently, MegaSquirt does not operate a drive by wire system. The early F-body and truck cable operated throttle bodies will bolt right on if your throttle body uses a three bolt pattern. Later LS series throttle bodies had a four bolt pattern. While factory four bolt throttle bodies are all drive by wire, there’s several aftermarket cable operated replacements out there.


Many LS powered cars and trucks don’t have separate gauge sending units, but instead drive the gauges from the Class 2 data bus using sensors the stock ECU reads. The MS3 has outputs to drive an electronic speedometer and a tach, and it is possible to modify the MS2 to drive a tach as well. For coolant temperature, your best option is to drill and tap the block for a second temperature sending unit for your gauge.