Engine swap

My truck listed above 5.8 EFI certain parts are NA runs great, tired of searching and waiting for parts to arrive, (this is my service truck for my business) must have running. Found a 1997 F350 RFI, exact same motor and transmission, started without hesitation ran as smooth as my 1994 while I stood there for twenty minutes, no issues, very happy, bought motor put in my 1994 with torque converter, had to use my 1994 harness plugged right in no difference, hesitated to start but did ran okay wont accelerate truck wont move, brought to running temperature shut off did self test for codes, started truck, wrote down and researched codes. Next morning truck turns-over will not start. What did I miss? Need real help, invested time and money and need my truck, tearing up Explorer doing service calls.