young olds

I helped a buddy do a 2jz swap in his mk2 Supra. We got it running on a stock ecu out of a 97 Lexus. He did bearings and a re ring, it blows black smoke out constantly and has a miss throughout the rpm range that feels like it gets worse as the engine warms up. I went through his wiring and fixed a few things to get it where it is now but we still have the miss and smoke. Engine was supposed to be a good running dealer replacement engine so the only thing that's new are the plugs wire and maf so far. Anyone have any ideas on this?