I purchased a 2001 F250 5.4 awhile back. Been working on a soft restore, it was in pretty rough shape. I decided to go ahead and slap a reman engine in it since it was at 200,000 miles and I did not have time for a rebuild. I got it road worthy a couple months ago and drove it around a bit testing it out. I had to put it back in the garage because the front axle tube on the Dana 50 was rusted out on the passenger side where the track bar and steering dampener mount. Got that taken care of and took it for a drive last weekend. It was running pretty good until I was going up a hill on the interstate. Started bogging down. It cleared up once I was off of the hill. It did it again on the same hill on the return trip. Got it home and parked it. Yesterday I go out to move it and its missing a little bit at idle. I go to move it around my driveway and it starts missing and surging. It will barely move itself around my driveway. I changed the filter thinking it was a fuel problem. No change. It has a new fuel pump. Coils. Injectors. MAF sensor. The dome light dims and brightens with the miss of the engine if that means anything. I am lost.

 

check charging rate?
Adjust fan belt, check alternator and battery connections.

 

After all that sitting I'd get the battery & alternator load tested.

 

I would check grounds I put a Fprd Reman in mine There is a ground on the starter, transmission and several on the firewall. Possible bent pin in the engine to firewall connector? most likely something you did unintentionally. Retrace your steps.

 

Any codes? How are the fuel trims?

I've been a fan of the ForScan software with a bluetooth connector to read live data.