On page 2 of this forum I posted asking for advice about almost exactly the same thing:
https://www.mk5golfgti.co.uk/forum/index.php/topic,134703.0.htmlI worked out that the wing at the bottom can have the bottom bolts behind the arch liner loosened, then pull the bottom of the wing away from the door and insert something in the panel gap so it doesn't go back again while you re-tighten the bolts. This worked perfectly for me - The arches were replaced on mine and not quite adjusted properly.
Personally I wouldn't touch the adjustment of the doors, since the change you made was to the wing and not the door, the fault lies with the wing fitment, not the door - Don't break what doesn't need fixing, you'll just have more headaches. Adjust the wing properly and pull it away from the door, then retighten the bolts. You may need to do more than just the bottom bolts on yours to get the adjustment you need, but mine was fine with just the bottom ones.