did you swap the ecu when you swapped the engine/tranny? if not you have an ecu for an automatic trying to work on a manual. that would cause some weird issues. it sounds like the ecu is running in "limp mode" meaning it knows something is wrong and is dumping a bunch of fuel and limiting the revs so you could drive it without risking too much damage. but unless it's throwing a code it's going to be very hard to narrow down because it could be just about any sensor.