Alright I finally got my new motor in it is a 02 4.6 mustang motor(factory rebuild) in a 97 150. On the first start only one side of the motor would run. So I swapped the coil packs from each side and it started up and was running great, but then it started to miss and run poorly again. I swapped in new coil packs and started it up and it was running a little rough. I ran it about 15 miles on the highway and it got stronger and stronger. Just wondering if anyone knows of a problem that may cause this because I am paranoid now. Pretty much everything is new except I used the old intake and port matched it. It has been down for about 3 weeks so my thoughts were possibly, cats backed up, bad gas, or ..... Everything thing else is great no check engine light and on the last drive it really set me back in the seat I just wanted some opinions because It has a lot of time and money in it to not be running right.

 

put about 50 more miles on tonight and looks like the computer might be correcting itself. It is running like a raped ape now. Thanks to all that have helped during this abortion. I'm sure i'll have more questions soon enough.