I have out my back right quarter window on 240z. i bought all new weatherstrippings and put them on. Now it is Tight.... i am mean too tight. I have the weatherstripping on right and solidly. However, even with me pushing the window in with everything i have it still will not line up with the holes. 

I compared the weatherstripping with the OEM on my left side and its definitely thicker. Anyone else run into this issue? 

Yeah it's damn tight. I remember it being really hard to get the screws in. Careful you don't cross thread them. Keep trying. Get a helper.

Yeah you might need a helper, I had to hammer the tabs a little bit, I think the last person in there messed them up. 
 

I also used new hardware, my old ones looked weathered from leaks, wanted to avoid stripping stuff.

I have seen people use longer screws to help pull the window in and then replace with the original ones.

 Warm up the rubber well and lubed well. Two or three people helps.  Seal from the inside after installed if needed. 

1 hour ago, 7tooZ said:

 Warm up the rubber well and lubed well. Two or three people helps.  Seal from the inside after installed if needed. 

Rubbing alcohol makes a good lubricant for installation. Then it just evaporates.