On my repop timing cover from cal pony cars all four bottom bolt are to long. When I looked both covers the bosses on the new one are shorter so I just bought shorter bolts. Is the boss on that water pump different there?
As long as they are not to deep and the bolt hole fit is ok I would put a washer on it just to help. They were done by a cut off wheel or air chisel to remove the rivets that held the ball joints on originally.
If I understand you right this was fine till you put in the weatherstrip and now it sounds like the weatherstrip is pushing the vent window frame at the top is that right? You can adjust the vent window frame in and out so it don't push as hard on the seal. I don't know if this can be done but...
Pictures would help. Did your door glass work ok before and your new regulator repop or OEM? How much gap do you have between the vent window frame and the Windshield frame or A post? You can adjust the vent window frame if you have room and the stops will help you get more in the back.