It sounds like you have a misfire, likely related to spark plugs. If they are over 25,000 miles they likely need replacement.
Reading the codes would 9/10 show a misfire. The misfire only occurs tuned because you are running nearly 2x more boost then stock, perfectly normal.
Over time the spark plugs gap increases, which is the cause of these misfires.
However, I would first, reinstall the firmware and software on the PROcede and do a reset.