Check that the metal channel the window glass is mounted in is adjusted as indicated in this diagram from the service manual:
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I made the mistake of not looking into this when I replaced my window runs & since the glass on my driver door had slid forward in the channel, the back edge of the metal channel overhung the glass & started shredding my new window runs.
Thankfully it seems to be working fine after correcting the channel position when I had to replace the window motor.
Having the glass out of the door also gives you an opportunity to thoroughly clean it, & make sure the window runs are fully seated in the lowest portions of the track. I didn't remove the windows when I originally replaced the runs & they were a complete bear to get seated in the bottom portion of the track inside the door.
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