Sounds like a fuel flow issue but as Arisley stated what is the alternator charging at?
I worked on a truck that would act up intermittently after it had been running after 30 or so minutes. New batteries and cables. If I hadn't caught it myself i would have never believed it was an alternator problem.
The truck sitting read 12.9v on just batteries. The alternator would discharge 13.9, good right. The truck started acting up again so I had two meters out as I swore it was electrical. Tested with the truck off- 12.6v on the batts. Started the truck and only had 12.3v indicating a bad alternator when suddenly it jumped to 14.3v and was charging. Tested the damn thing for what seemed like a thousand times with no problem, charging great then Bam, it dropped again then suddenly started charging. Anyway, replaced alternator and problem hasn't returned.
Weird as they normally just quit charging but I caught it by a fluke.
Still thing you have a bunch of crap in the system.
Have you thought about back-flushing all the fuel lines?