Cummins Surge

Merry Christmas to all! I have a 04 2500 Cummins auto 3.73 with 25k.
It has never really run up to snuff. Recently, the dealer found a
problem with the transfer pump letting air get in the system. He
replaced it with an in-tank pump and that has helped. However, it
still has more vibration and noise than some of the other late Cummins.
Pulling a 12 ft flat-front cargo trailer from ne SC to Pascagoula MS
(70-75 mph), I got 12 mpg. (I am with a SC Baptist Disaster relief
unit). On our first trip (to Columbia MS), a V6 F150 pulled that
trailer and I pulled my 22 ft gooseneck and tractor with a front
loader. I got 8.8 mpg for that trip. Now for the question: After a
minute or so warm-up, I gently ease up to 55. After about 5 miles and
getting up to 60-64 mph, the engine starts surging (kind of like 70s
cars dealing with polution controls) and continues for 5 to 9 miles.
Colder weather seems to be worse and the problem seems to be getting
worse. Wonder what? Changing the fuel filter had no effect. Thanks
Mark31