Have you performed a VGT relearn? My truck had been doing the same as yours for the last 2.5 years, so I did the relearn last week and it appears to have solved all of my boost problems.
The following is from Diablosport Predator Update for 04 Truck - Ford Truck Enthusiasts Forums
The low power and lag problem could be a result of the sevice "Tech" not performing the VGT re-learn strategy after flashing the computer. Here is the strategy you can perform it.
KAM (keep-alive-memory) reset & VGT learn procedure
1. Drive the truck until the engine and transmission have reached normal operating temperature.
(The VGT learn procedure requires that the oil and coolant temperatures be at normal operating temperature)
2. Flash truck back to stock (Only need to do this if running a tuner or module)
3. Turn on the headlights
4. Disconnect both batteries
5. Short out + to - battery cables to each other (Make sure both batteries are disconnected before doing this).
6. Let truck sit like this for 10-minutes
7. Turn off the headlights.
8. Re-connect batteries
9. Cycle the key to the run position twice. Pause in the “ON” position each time until the wait to start lamp goes out (minimum 5-seconds) and pause in the “OFF” position each time for 10-seconds to be sure the PCM has "gone to sleep".
10. Start the truck and let it idle for a minimum of 5-minutes at normal operating temperature. This allows the PCM to learn the EGR valve closed position value. Also you will likely hear the turbo pitch change several times during this period as the PCM learns the necessary duty cycles for accurate VGT control.
11. Complete the road test Drive Cycle:
15 miles of mixed driving (*should* be enough in most cases) to allow the PCM to "re-learn" its adaptive strategy.
Note: Anytime the batteries are disconnected, the PCM will throw the P1000 code until the “Drive Cycle” is completed.
As for the Tow/Haul mode, the transmission must re-learn your driving style and loads hauled again as this was cleared when the truck was re-flashed.
Give this a shot if you haven't already. It worked like a charm for me.