I have never done one of these windows but using just normal door adjustment thinking, can I throw you a few ideas?
If the right passenger lower corner is out away from the mating area too much, you need to bring out the top of the drivers side. Again, just using door basics. The center has only the arms from the regulator holding it in the center right? If this is the case then it "pivots" on that center in the bottom.
If you bring out the top left, it will pivot on the center bottom and bring in the right bottom.
However, if you put the frame EXACTLY where it was before changing the rubber, then you have a binding problem of some sort where the rubber is holding the frame out. This would probably be happening up on the piller on that passenger side or towards the center of the bottom. That is something you can look into.
To check if the rubber is sealing too tight or not tight enough, you can close the window down on a sheet of paper. This paper should probably be able to be pulled out without a real lot of resistance. I would think, again I have never done one of these windshields.
Have fun
