the egr would cuase a sluggish condition, then power surge
with the new ford reprogram, the EBP is cut out of deciding boost and other things, and the signal is substituted by the pcm looking at a few other sensors and coming up with an ebp reading.
ive seen some trucks come in with lack of power, and the reason why they werent running 100% was because an injcector or two was droping out, even though the owner didnt feel a miss...
my dealer readily throws turbos on trucks, we have an underboost/overboost code, or the MGP sees abnormal boost numbers, 9 times outa 10 that trucks geting a turbo, i did one just today, the vgt was sticking, witch is what fails on most turbos. with 6.0 trucks you really have to be mean to them to keep the turbos from failing, if you granny foot the truck, you will be doing aturbo on it every 50k or less...but my bet is your power loss is probably a turbo issue, are you hearing the infamouse turbo chatter, where the turbo vents the boost back threw the intake, at all?