my car did the same thing with the old swap. i really just came to a conclusion that i had bad compression and the motor had stopped making power as it used to. but i never knew what was up with that swap. it basically ran like shi.T!!! eventully one day my timing fu.cked up and i had bent my valves! but since you said the timing is good, i think your motor is losing compression. but i may be wrong. gl with getting it fixed!