dzidaV8, first I want to emphasize - great work! I have a 2002 0411 PCM I thought to play with your XDF. I have a 2000 Silverado that I'm trying to upgrade to the 0411. :)
Your XDF has helped tackle a lot of the minor changes, but there are a few that does not seem to be working correctly:

In the Engine DTC Processing Enablers I tried to change
P0106 Manifold Absolute Pressure (MAP) Sensor Performance
P0741 Torque Converter Clutch (TCC) System-Stuck Off
P0752 Shift Solenoid Valve A Stuck On
P0757 Shift Solenoid Valve B Stuck On
P1683 Control Module Ignition Off Timer Performance

And in the Engine DTC MIL Enablers I tried to change
P0741 Torque Converter Clutch (TCC) System-Stuck Off
P0752 Shift Solenoid Valve A Stuck On
P0757 Shift Solenoid Valve B Stuck On
P1683 Control Module Ignition Off Timer Performance

I made the changes in TunerPro (along with multiple other calib data as well as other DTC options). All the other small changes seem to work well (as the change is reflected in EFILive). Checksum changes and looks good. When I changed the above nine different DTC, TunerPro shows a change, but EFILive does not show the same change. Perhaps double check on the location of these data bits?

And another odd thing - I changed the VIN in TunerPro. The *.bin shows the edited VIN in EFILive. I flashed the *.bin to the PCM. Then I re-read the *.bin from the PCM and it did not show the VIN number changed. I used Antus's tool to change the VIN and that was successful.

The truck runs great with the 0411 PCM so far, but not quite perfect yet. No SES light and no drivability issues that I see so far, but I'm having a phantom DTC lighting up the battery in the Message Center despite the voltmeter showing good voltage. (I think) I have tuned off the DTC for the battery, but still getting this message. I'm still investigating this. (Switched back to old PCM and no battery message.)