Jason,
I believe I have felt the same thing you were talking about, with my rig.
2001 truck, auto trans, with Banks Power Pack, Full instrumentation, plus fuel gauge. Was towing a 7,000 lb travel trailer to Idaho. Everything was fine, no problems.
After a fuel fill up in Burns, OR, I noticed a difference.
Under a load, turning about 2,300 to 2,400 RPM, between 55 to 60 MPH, fuel pressure good, about 10 or so PSI. Temp outside was hot, upper 80's.
After coasting, slowly starting to speed up, could feel the engine miss, something like a gasser would do.
Before my trip, all filters were changed. Primary and secondary fuel filters changed, K&N air filter, cleaned and re-oiled, engine oil changed and new oil filter installed.
Did change out the VP44 I. P. just a little while ago, but never had any problems. Got an upgraded one from Blue Chip Diesel in New Hampshire.
When I have the pedal at WOT, no problems, fuel pressure 8+ PSI, and no missing, everything fine.
Back off to coast, then slightly powering up, could feel the hesitation. No, it was not during, or when the AC was on.
Sometimes AC on, sometimes AC off.
Plugged in the scan tool. No codes came up, says everything fine.
During my trip, my eyes were like a Halibut, one eye on the road, the other on all 5 gauges !
Fuel filters have maybe just over 2,000 miles on them.
Any additional thoughts, from you or others ?
Peter