My 01 is a turtle. You can't pass anyone it is so slow in acceleration. Yet, it will pull a 12,000-pound excavator up a hill no problem and still slowly accelerate. No codes, no misses, 15psi fuel pressure, and 25 pounds boost. Like I'm not getting full throttle. Any ideas?

 

25 PSI of boost at least makes me think it is getting decent fuel to the injection pump.

Have the ETG temps dropped along with the power you have lost?
Did it act this way before you installed the stage II auto?

 

The APPS is getting full travel. Visually verified and my scanner shows 0-100% on throttle position. The EGT peeks out at about 1050°, always has. No difference with the transmission. But may have happened when the IP was overhauled. Hard to tell, I rarely mash the peddle all the way to the floor except while pulling a load.

 

My '01 never got above 1,100 EGTs either and it would tow a 10,000 trailer at about any speed I wanted, up about any hill.
Sounds like you are getting enough fuel to make some decent power.

Is there some drag in the powertrain somewhere? Brakes? Transmission?