2006 6.0 Runs rougher the longer it runs

Hello I am new on this page and finally broke down to get some help with my 2006 F-350 6.0 PowerStroke with 152,000 miles. It has head studs, EGR delete, 4 inch straight pipe, AEM Intake, and an Edge performance system and 58v ficm. Recently I did head gaskets on this truck and before starting the job the truck ran great but the head gasket got to the point where we could not put coolant in it so it had to be done. After completing the job the truck is not running very good. along with head gaskets I did both fuel filters (Duralast FF779DL), oil filter, oil change, oil stand pipes and dummy plugs, ipr screen, injectors external seals. Did not touch the injector internal seals or nipple seals.

The truck starts up after cranking for a few seconds and runs OK but sounds like it is missing pretty bad and the warmer/longer it runs the worse it runs. It also seems as though the longer it runs it gets louder like there is more load or resistance on the engine.

The only code that is current is for cylinder 3 contribution balance which I would believe to be an injector but that alone should not cause it to run this rough. (all 8 injectors are original still)

Couple things i noticed when starting and running:

• when I turn the key to on and the FICM goes through its precycle the FICM voltage drops down to 40 sometimes a little lower sometimes higher then slowly goes back up to 54.5 but never reaches 58 volts. keep in mind this is a 58 volt FICM. While the truck is running it will sit around 54 volts. After that i replaced the power board with a new 48 volt power board but it did the same thing drop down to 35 volts on precycle then slowly go back up and sit at 48.5. I don't know if that is normal or should I just replace the whole FICM unit.
• Also when I turn the key to turn the fuel pumps on i can hear little air bubbles in the fuel tank and the HFCM sounds like its trying to push air. I triple checked both fuel filter caps and o rings along with fuel lines to make sure they were all seated right. with a fuel pressure gauge attached to the check valve on the secondary fuel bowl the fuel pressure reads 65 psi while idling. There is bleed line attached to the fuel pressure gauge which I would use to bleed air out of the line but the air slowly comes back. I don't know where to look for air getting in the lines at this point i'm thinking the pick up in the tank or something like that is pulling air. ( the tank is 75% full). I bleed the air as it runs.
• IPR sits at about 30% at idle and icp reads ~850 psi at idle.

If anyone could help me out with this it would be much appreciated. I will keep this thread updated if I find the issue.