First, you need to check for codes thrown or about to log a code. You need a scan tool that can read shadow codes, not just OBD-II generic codes.
It really sounds like you have a misfire going on. Could be bad/worn plugs(they should be changed every 30K to 45K, you might start there) or maybe a bad coil. Of course a miss could also mean a bad injector or spray pattern - but that's not so common.
Could also be something as simple as bad fuel quality. Try switching fuel brand for a few tanks.
What about the HPFP ? Has that been changed?
You really need to have the codes read - before you dive too deep into this issue.
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