If you've gotten this far then it should be an easy fix.
Start the vag com, go to 1-engine, change the soft coding from value 1 to 2. This will make the ecu think it's for a manual. Shut off the car, check it again and it should be 2, for manual.
The limp mode could be an overboost. If you have a boost gauge it can help you figure out if there is a problem. Probable cause since you checked the vac hoses - vac hose that wasn't put back on the right spot when you did the swap or stuck actuator. I think there's a writeup for checking and replacing the turbo actuator. If this is bad then a good n75 won't move it correctly. Try squirting some PB Blaster at the pivot points and see if it helps.
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