How long has it been doing this? Also what year? Do you have a CEL associated with it?
I have an '03 GTI 1.8T with the 5-speed and mine did something similar. But mine would do it in the lower gears. When I'd accelerate it would lag and stutter right around 2k rpm and about 3k would be fine. Once I'd get in 4th or 5th it was fine. Mine progressively got worst and then finally a coilpack went out. In my case that coilpack would intermittently work for a brief moment and then be fine. The stuttering I had was from that cylinder not firing for just a brief moment. But once it fired it would be fine. I didn't have a CEL until it finally stopped working all together.
I limped it to the dealership, bought all new coil packs, popped the new ones in, and all was fine after that. Not sure if this could be what is up with yours. A set of new coil packs is about $100 and 10 minutes of your time to install them. Might be worth replacing them and see. Best case is this fixes it. Worst case is you spent $100 and its not fixed, but you'd still have new coilpacks.
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