ok ive got a 96 sport 1.8l implanted in my 94 geo tracker..i put the complete wiring harness from the donor vehicle into my tracker...it was originally a 4-speed auto,..i used my 5-speed from the tracker with a modifyed flywheel and bushing,..i cut out all the auto trans wires and trans ecu from the harness, but still using the auto ecu for the rest of the engine...im getting a check engine light and decided to pull codes today,...comes up as p1600, which would make sense beings how there isnt a auto trans in there anymore...thing is,..even after its up to normal driving temps,..it idles at 1100-1200....first morning startups its 1500-1700...which is fine and appears to be normal...
does the auto trans ecu controll any of the idle speeds by chance?...

p1600 is the only code comming up...everything else wiring involved is hooked up in there desitated place and working....thanks in advance