I would invest in a vagcom cable and scan for faults, but if your re-mapper was any good they should have done this before getting stuck in.
1.8t are not the smoothest engines, but from what you are saying yours seems to have an issue, likely suspects are engine breather system and vacuum pipework.
Breather system pipework dissolves itself from the inside out -mine felt off for weeks before the check engine light came on only to find several holes.
Also the vacuum pipework just turns to dust.
Best to just replace with silicone-
Breathers, I used a creation motorsport kit, but they do require some cutting to fit.
Cant remember the seller, might be mr.silicone, but I got a great engine kit of silicone pipes and just replaced all the old rubber pipes