Re: window gap
You could try just dropping the stops about a mil., whats supposed to happen is that as the door is closed it clears the seals, and then as it closes a little "up/down" device raises it 2mil to seat into the channel. The device works with a microswitch and isn't easy to get at. Its probably worth removing the door card and doing the stops first. I suggest shut the door with the window open, then raise it and adjust the stops to suit as a first step. It can be quite time consuming to get the window just right, I recently had to do mine after having a new side window fitted by an "expert", when he left the door was shut, as soon as I opened and closed it I had exactly the symptom you describe. I spent ages trying to adjust it, but eventually gave up and started from scratch with the glass out. I followed the instructions from the workshop manual which the expert had spurned, and hey presto! The window fitted perfectly first time, no gaps, no noise, without any further adjustment. Good luck.