Diesel Bombers - 2003 7.3 Powerstroke Troubles

Started having overheating issues 3 months ago. Two mechanics decided it was a blown head gasket. Just got repaired with new head gaskets, head bolts, injector cups and so forth. Replaced coolant overflow reservoir and drove last night with no problems. Started to work this AM with no problems but when I was almost to work it started running rough. I can accelerate fine but when it shifts gears it starts to run rough. Has new fuel, air, and oil filter. No clue what the problem could be as it seems to idle fine and setting with RPM increase there seem to be no issues. I'm about to go crazy as I have already dumped over $5000 in this issue and still not correct. Any help would be greatly appreciated.