Diesel Bombers - Hard starts/missing when cold

I have a 2006 Powerstroke with the 6.0L diesel, obviously. I have done lots of work to it, as follows, Sinister upgraded oil cooler, Sinister upgraded egr cooler, upgraded dummy plugs, BWD egr valve, K&N Cold Air intake, New EBP sensor, new IPR, Rebuilt Hi pressure oil pump, Had FICM repaired (a few capacitors had broken off)
Anyways, after all the work was done, I took the truck on a long road trip and threw the famous P0401-insufficient EGR flow. I cleared the code and ran the KOEO and KOER tests and everything was fine. A few weeks later, I had the same code. I swapped the EGR and cleared the code and everything went great. However, about 3 months later, I threw the code again, during in-town driving (top speed 45). I cleaned out the tube that holds my EBP, which wasnt all that dirty, and replaced it and it ran fine.
On to the real problem- Currently, starting about January, I have had slow starts, almost as if the engine is working itself up to idle. There is no throttle response for around 10 seconds, and when there is throttle response, it feels as if half the cylinders are missing, but only at higher rpms. Once I hit the road, the truck will wind up around 3500 rpm before shifting, and nearly give you whiplash when it shifts. After the truck warms up, roughly 5 miles down the road, all this stops and the truck runs great. I keep the truck plugged in below 50 degrees. I have tried lots and still cant seem to figure it out!:dang:
I apologize for the novel, but I wanted to be specific and clear. All input is greatly appreciated! Thanls!