Idles and runs rough when warmed up

2 weeks ago, did a motor swap on my 02 grand am gt 3400, with a 05 3.4 3400 engine with about 116000. Car itself has 170,000. Runs perfect when cool or cold. When warmed up it will be rough idling and run like crap. When it warms up id doesn't seem to be running off all 6 cylinders. It still drives and does not die. When kicking it into passing gear it just doesn't have the power like it does when its running normal or when its cold
Already changed upper o2 sensor, put lucas fuel injector cleaner in it, and changed the mass air flow sensor.