I had the same problem. My seals came from Craddock and I was of the opinion that they were too stiff rather than too fat. I solved it by completely slackening off the bolts that hold the glass to the track runners. I then closed the window so...
I recently replaced both my seals, and the cracked drain points and cleaned out the pipes with compressed air, recovered the headliner, put it all back and it still leaks! I bought my seals from Craddock and in my opinion they are too hard to...