Ford 6.0L Power Stroke Diesel :: Missing Only When Engine Up To Temp

To start off. I have a 2004 F350 with the 6.0 in it which just had a top end rebuild done on it due to the head gasket blowing on it. During the rebuild the EGR cooler was also deleted, ARP head studs, Heads were milled down to make them flat (shop said they had to take 9 thousands off to do so), new up pipes installed, new back pressure sensor installed due to the plug head snapping off, new glow plugs, new glow plug rail harness, oil rail rebuilt due to bad o-rings on the ball tubes, injectors were installed with all new seals and had polished the spool valves hoping to avoid stiction (however its spelled can never remember), and lastly the EGR was deleted electronically with tuner. Also had to get 2 new batteries as they were stone dead and would not take a charge. And had to get a new alternator due to low output. Not sure if the alternator killed the batteries or the batteries killed the alternator either way it needed replaced to.. Unfortunately after i got that fixed i had to get a new starter as it died 3 days later.

Ever since its gone back together Ive had a consistent intermittent miss with the truck. Ive searched every article i can find but seems most complain about misses when cold. Mine is the exact opposite as it only does it once the engines up to normal operating temp. It accelerates hard and fast like it has no issues. While its cold it doesnt miss at all. Once its warmed up sometimes while cruising it will feel like its missing on every cylinder or better description would be as if your driving on a cobble stone road.. If you mash the pedal for a couple seconds till it kicks down and raises the rpms it stops.. Its most prevalent at idle though.. You can literally hear the difference in the engine when it starts missing. Truck will shake as if its got a large lopey cam. Odd part while sitting at idle it will cycle back and forth between running smooth and missing. But same with at cruise as soon as you get on the throttle it goes away. If its doing it while sitting idle at a light, it will take a couple seconds once your on the throttle for it to smooths out. But always does.

Ive tested the Ficm hot and cold, KOEoff and KOEOn.. getting a steady 48v from the main board.. Scan gauge says the Logic boards reading steady 13v... Also from the scan gauge it says my ICP pressure is in the 640 range at idle (full throttle highest ive seen is 3600psi so dont think its a pressure leak) and volts bounce between .80-.90.. but oddly once it starts missing the ICP pressure jumps up 20 psi.. IPR at idle reads 23.5-25.5.. at cruise its up around 45ish.. fuel pressures said to 70 psi.. which its usually around that most times, cruising itll be around 66psi. I had 3 injectors replaced not this past spring but the year before (ironically same symptoms).. Injectors 5,7,8 were replaced then.. ICP sensor was also replaced at the same time as it split and shorted out the connector which was the initial reason i took it in that time since it was dumping the oil on the ground.

I dont have any way to perform a cylinder contribution test and after spending 6K on a rebuild I really cant afford to take it in to have someone else do it. A local guy was able to scan the truck for me but he couldn't do the contribution test either but was able to buzz test them. Everything passed there but we also found some hidden fault codes my code readers did not find. The ones we found hidden said that injectors 2, 4, and 7(again??) are reading low contribution. Of what I've read 2 & 4 sit on either side of 7 in the firing order so have wondered if they're not pulling down 7's results.

I really cant afford to replace the injectors till near the end of next month. Is there anything else I can look at that might actually possibly be causing false readings or intermittent misses only when warm.