What about all the sensors and actuators? Were all those swapped along with the whole engine or did you keep the old ones and move them over? Its possible its just an engine management issue, could be a bad map, o2, IAT sensors, or possibly a bad fuel injector. Make sure everything is plugged in, Also make sure the each injector harness is plugged into the correct injector, i've cought a friend's own idling problem with a harness swapped across the wrong injectors after he did some work.

Sometimes it could turn out to be a big problem, or it could be a very ez simple issue, it can be easy to overlook simple things, i've made that mistake in the past.