I would suggest using the rubber jack blocks that come with the windshield seal (3M supplies them) to support the glass rather than the metal clippy things. I just put a used back glass in my Challenger and the blocks centered it up just right. The clippies would have been a good 3/16" too low.
I noticed that the side gaps are pretty big once it's in, but I got a good seal anyway. (I DID have to add a little extra seal to the sides, toward the bottom.)
I left the paper on the seal and set the glass in place to check for a consistent seal before getting crazy and sticking it in permanently. Removed glass, added extra stickum, re-applied paper strips, test fit again, etc.
It's an easy job, but then again......not really.