Upgrade from AEM EMS
 

I am currently running the EMS4 in a 1990 with a 2000 engine. I know this is a stupid question, but I think I remember that I should go with the car year over the engine year for choosing the ECU mainly due to the wiring. Can someone confirm this. Also, I am assuming some custom wiring may be needed since I am supercharged and running the various required sensors beyond stock set up. I think I remember a little extra wiring when I installed the AEM, but its been maybe 7 years since install

You'll want to order an MS system that matches the harness that is in your car. Just use your factory IAT sensor wires (the ones at the AFM) for your aftermarket sensor if you have that run separate already.