I went through this same mess when I rebuilt my M1028. The aftermarket replacement rubber is too big and there's no way to glue the dang stuff on where it will stay. After buying the aftermarket stuff from two different outfits and then throwing all of it in the dumpster, I decided to do some research and see if I could find some NOS OEM rubber. I learned that up until the 1984 model year, GM offered all the factory parts to rebuild the vent window assemblies. However none of that stuff is still around, even from the vintage OEM parts dealers. Then beginning with the 1985 model year, the individual parts were discontinued and only the entire vent window assemblies were offered. The part numbers were, and still are, 15634471 for the driver's side and 15634472 for the passenger side. I found both at Boomershine in Atlanta, and after selling a shotgun and a log splitter, bought both for $550. I have been ridiculed for paying so much for these but HEY - I plan to be flat broke on the day I die, so WTF? I now have brand new vent windows and I love 'em.
Hope this helps.
