A typical mechanic is not going to be able to help much with an after-market bolt-on custom tuned turbo kit. If you do decide to take it somewhere, find a performance shop that specializes in designing/installing/tuning custom turbo systems and kits.

The only way your vehicle could have gone back to the stock tune is if you took it to a dealer and they flashed your computer with an update, or if you specifically installed the original backup with the InTune.

It is possible that a problem with your current tune caused long term fuel trims to gradually adjust to extreme values in a certain engine load/speed area of the maps/tables, which could explain why you did not initially experience these problems. An easy way to test this is to simply install the most recent tune you have from Prodigy again. This will guarantee you have the right tune installed, AND will reset all adaptive memory for a fresh start. If it starts driving good again, then you know for sure the tune was the problem.