There's an adjustable stop at the top
They are actually little window guides in the frame. When they need adjusting or refitting they can make the windows noisy, hard to move and give problems with draughts.
They may be causing your problem. I'll try and copy the relevant technical bulletin for you (163?) if I can find it. It's difficult to explain how to get at them otherwise.
The alternative is to elongate the holes for the widow pillar and motor to give some 'adjustment' although it sounds like you've already tried that.
Also make sure that you are getting the full range of travel from the worm drive, otherwise no amount of adjustment will help.
When you refit a window there are often draughts or whistles as the seal 'moulds' itself to the previous glass position and it's always hard to get it to sit in exactly the same place. A new seal might help but they're really expensive!