Rep Power: 0

I have a 97 Honda 3Dr DX, 5 speed. I recently pulled my blown engine and replaced it with a low mileage 2000 engine out of an automatic DX. The only differences between the engines were the 2000 had a different plug on the distributor and the IAC was different on an automatic. I changed out the distributor plug and replaced the IAC with one from a 5 speed. The engine runs great except when it reaches running temp the idle goes up and down. I am showing no trouble codes. I installed new O2 sensors and cooling system checks out. I checked for vacuum leaks. My next step is to adjust the set idle screw. My thinking is the automatics idle is set different then a standard. Does anybody know what else it could be?

 
Rep Power: 291

Idle surges could be a number of things,
With my quick 5 second searching of civicforums, i saw either O2 sensor, or bubble in coolant system

so meh...look around