Rulebreaker

I put the car on the computer and I was given a MAP code.

Pulled a bad 2.5 and put in a 2.2, It runs but runs rough under 2000 rpm. I have spark to all 4 and good compression but it seems that whatever cylinder I hook the green fuel injector wire to is the cylinder that miss firers. If it's on cylinder two and you unplug the injector wire nothing changes, If you put that wire on injector 4 and then pull that wire nothing changes. You pull any other wire it dies. I am using the original wire harness and the old motor did not have a rough idle, so what am I missing here? The other thing that puzzle's me is on cold startup it runs supper smooth until the computer decides to lower the rpm and then the miss/ shake starts immediately.