Cool! If you are lucky you won't get converter codes, I don't and I don't have them either. Just be sure you have all 4 O2 sensors installed, with them in the proper locations (like fronts in front, rears in rear, and on the correct banks). Also, I bet part of your running issue is due to the lack of the Mass air flow sensor.
By the way, did you ever figure out which wires were different in the 42 pin plug? And is everything working for you now?
Be sure to put a link to this thread in your engine swap thread!