1996 F250 engine swap problems

My husband bought a 1996 F250 with a 460 engine and a 5 speed manual transmission. the 460 was blown, and he a great 300 6 with a 5 speed out of a 1992 F150. He swapped motors and tranny, and it would start but ran horribly, like it was missing on about half the cylinders. Now it won't even start. Anyone have any ideas on what could be the problem? We are thinking maybe ECM or wiring harness. Thanks for your help.

Bumping up, hoping someone can help.

Bumping up, hoping someone can help.

I have never done the swap but I would check into a ECM for the 300 engine. You may need wiring harness also since 92 is a obd1 system and 96 is odbII system. Is the ecm available out of the vehicle that the 300 came from??

Yes, it is available. Thanks for your help, I didn't know about the OBD system being different.