Ok so I pulled the EGR valve last night and cleaned it using carb cleaner, it didn't apppear to be that bad, I made sure it wasn't stuck or anything. I cleard the DTC's and then drove the truck to work this morning, it is still acting up. It is running better than it has been, but is still loading up or something, the boost pressure comes right up but still putting out a lot of black smoke for a minute and then you can really feel it take off. It does have constant boost pressure driving on the highway now and goes up and down depending on the load being put on it. I checked the DTC's when I got to work this morning and still have the P0046 and agan the P2262 showed up this morning.
The fuel milage is also coming back up, so the truck is running better.
Sorry to be a pain, but what do you think i should try next? Any ideas?
Again thanks for all your help.

At this point, you've tried nearly everything I can think of to rid of that p0046, and the only thing left in my eyes is the VGT solenoid itself. I'd have a tough time swallowing buying a new one... myself I'd probably try and find a known good one on ebay, or a buddy with a 6.0 and swap it around. It's either that or the turbo itself is just past it's prime. Black smoke is telling us it's fueling up but the turbo can't catch up and clean it out. I'd be tempted to try a VGT solenoid now.

Did you ever pull the turbo and clean it? I know I asked, but I don't remember seeing you post that you had done that. If you haven't done that, that's your next step.

Mike, I did pull the Turbo over the weekend and cleaned it. I do have a buddy here at work that has the same truck a year newer than mine, we did pull the MAP sensor off his and tried it on mine a week or so ago. I will talk to him and pull the VGT solenoid off this afternoon and try it on mine, I will let you know this afternoon if it worked or not.
Will let you know how it goes shortly.
Thanks again for all the help!!!

Awesome, definitely try the VGT solenoid swap then and see what happens. Hopefully that's all it is. Not common for them to go out, but it does happen.

Mike, finally getting back around to let you know how it went with the VGT Solenoid, I actually purchased a new one from Ford and no luck. I'm just not convinced it is the Turbo itself, it always has boost, just not as much as it should when I first start driving the truck, after about 15 minutes of driving something will come loose or something and then the Turbo works fine, once it starts working it works just like it should until I park the truck and let it set long enough to cool off, then it will start all over again. Is there anything else you can think of that might stick and then start working once the truck warms up? Maybe it is just that the turbo is shot or sticking. I just want to make sure I have checked everything before I invest in a new one, I would hate to purchase a new turbo and find out it is something else. Should I take it to a dealer and let them check it out first?
I am just looking for your opinion on what you would do next.
P.S. I have cleaned the EBP tube and sensor, pulled and cleaned the EGR, Checked the MAP hose and sensor, pulled and cleaned the Turbo, tried a new VGT solenoid.
The only other thing I can think of is if the piston that is across from the VGT solenoid is sticking, have you ever seen or heard of that happening?
Thanks for you help!!!

The only other thing I can think of is check over the wiring harness with a fine tooth comb, or maybe even try swapping it with your buddies wiring?

I had the EXACT same problem before, where boost would fall to 0 cruising down the road, roll into it and leave a black train for a mile and then finally it would light and go. Mine didn't really throw any codes, but when I started monitoring EPB sensor, it would go from full max value to full min value and just kept bouncing up and down. I knew something was up. Went to pull the sensor to clean it and noticed the wiring had been chaffed right through on two of the three wires. Pulled it apart, sealed them back up, and wha-la... truck ran fine after that.

These 6.0's are really picky with wiring harness'. Sometimes even if they appear ok, they're not. Always nice to have a buddy with a 6.0 to swap parts with.. :w2: