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