Check your Short Term Fuel Trim [STFT] while the car is warmed up and idling. They should be between -%10 and +%10 for both sides, and should bounce around a little. You can play around while watching these to find out where your vacuum leak is at. Or you may have another problem like too small of injectors or weak fuel pump or something else. I have a bunch of experience with these while they are living in their original vessels. The problems you are having may be related to some parameters being changed with the swap.
How does it run?