4.0 swap bad miss while driving

[lambo_king1]

I had a 96 4x4 5 speed with a 3.0 in it that started burning oil pretty bad so I decided instead of replacing the 3.0 I would just buy a donor truck with a 4.0 and put that in. so I found a 97 explorer 5 speed 4.0 with 130,000 miles that was wrecked. I pulled the 4.0 and threw it on the engine stand and put a gasket kit on her (head gasket, valve cover, water pump, both intakes, oil pan) probably missing some but you get idea. I got in and all hooked up swapped the computer and everything required. the engine will idle great and rev up just fine but while driving it has a very bad miss and it cuts out so badly you can't drive it. I have a suspicion that the cam position sensor is not in the correct orientation. can anyone confirm the CPS causing this symptom? any other ideas? does anyone have a fool proof way of installing the CPS? thanks in advance for your help. anything is greatly appreciated.