1995 escort transmission swap

I have a 1995 escort with a automatic transmission that I'm going to swap to a 5 speed stick. What I'm trying to find out is this going to affect the EEC unit with the automatic transmission electronic wires no hooked up anymore or will it just let the Service Engine Light stay on.

I am not sure about the EEC, but the PCM (on the floorboard behind the dash) is different. Yes, it will cause your Check Engine light to stay on.

Hey Mightymoose,
So if the pcm is different. Would it hurt anything to run the automatic pcm with the stick shift. I don't care if the check engine light stays on so long as the engine runs fine. What you think?

The engine should run fine.

It isn't just a matter of swapping the transmission though. The job will be a bit bigger than that to get the shifter, clutch, etc. all installed.