just replaced my motor, question about why its idling rough.
spark plugs replaced (ac platinums)
new plug wires 6k miles ago
new fuel rail and injectors
new fuel filter
my a/c is disabled and removed
short ram intake
2200 OHV out of a 2001, on my 2000 cav.
Easiest - > More advanced
Check all your vacuum hoses for leaks, and that their hooked up. Especially the one going to the FPR
Test Spark (make sure all 4 are sparking, one may not be), and clean the spark plugs with a brass brush if their fouled)
Check fuel Pressure(find out what factory) is. Your pressure should build when you turn to the run position and then stabalize, if it continues to drop after stabilizing it could be a bad sending unit not holding the pressure. If it drops try pinching off the feed line, if that stops the drop its the sending unit, if it doesn't try pinching off the return line, if that stops it its the FPR, but typically when an FPR fails you'll get gas in the intake and some afterfiring.
Hope this gives you a place to start.

-Chris
thanks for the thoughts! ill give a few goes around with it. any other ideas?
i have been looking at new coil packs also.
its behaving similar to before the motor swap. im guessing that means its a sensor of some sort. im going to start with the idle control sensor and go from there.
spark is good across the board, and all vaccuum lines seem to be in tact and connected properly