ge_elle

I bought a wrecked 2003 f150 with good power train that ran great before I replaced it into the 97 f150 and now it runs ruff at a idle and when I give it gas it runs ruff as well. I replaces the motor, trans and transfer case all at the same time. The new motor had 87,000 miles and the 97 had 208,000 miles on it. After replacing the motor trans on it, all I could see that was different was a plug that came up the right side of the motor that connected under the power distribution relay for the starter and the power that went to the fuse box. The plugs that was on the 97 was 2 bigger square ones with 1 smaller round one, and the one on the 2003 had the same 2 big square ones with the exception of the small round one was replaced with a larger square one, so I replaced the entire wire harness that goes under the hood and wrapped around the front of the radiator and almost back to the battery where it began. The fuse box was different and a lot of other plugs were different, (but didn't have anything to do with the running of the truck) like the horn and the impact sensor for the air bags, so I changed them from the 2003 over to the 97, that way everything worked. But after all that, I finally started the truck and it ran ruff. Does anyone have any ideas and do I need to change over the ecm or any other control module? I actually replaced the module that goes under the glove compartment and connects to it from behind the battery tray with a 10mm bolt that connects the harness and connector to the module and it did not start when I changed it out. So I put it back to the original one back in it and it still runs ruff. I would appreciate any help or advise on the matter. I thank you for any help you can give me. Thank you for your time.