I am gonna try and explain this the best I can. I have a 99 accord with a v6. The motor was a distributor motor. The motor I put in is a coil pack engine from I think a 00 accord. I swapped the ecu and harness as well. Had a few problems as far as the immobilizer because the wire for the immobilizer was in a different spot on the plug from the 99 to the newer engines.

The issue I am having now is the surging idle. I have been over every cause of the surging idle. The tps sensor, the iacv, coolant and many others. So I pulled up the wiring for the ecu again and found that I do not have a wire in the plug for the tps output signal. Its in connector A which is the one from inside the car. The only harness I didnt change.
In the #31 spot on the 01-02 models is a yel/grn wire for the -throttle position sensor output signal-. The ecu I have is from a 02.
I hope I have explained it the best I can. The only thing I can think of is that I am going to have to use an ecu from a 00. Does anyone else have a thought?