IF your issue is that the window glass does not TOUCH the upper weatherstrip, or barely touches it, or goes into it but doesn't seal well, but is otherwise aligned with it-both side to side and fore and aft, YOU MAY GET LUCKY and just have to adjust the glass guides, inside the tailgate. (Those almost always work the same way the ones in the driver and passenger doors do-on Fords anyway.)
The UPPER channel/weatherstrip (the glass run channel material) often takes enough of a "SET" to the position of the OLD glass gets flattened or worn enough that it doesn't make good contact with the NEW glass-even after adjusting the glass guides. (And adjusting the glass guides doesn't
really fix the problem of the glass having too much play from worn/flattened glass run channel when its in the upper channel.)
The second possibility is that the material LINING the metal window guides (AKA glass run channel)
in the tailgate is either worm enough, torn, or missing and that the glass has too much fore and aft play while its inside the tailgate. THAT would not be unusual on a vehicle that age. If the glass can move around fore and aft when its inside the tailgate, that might be the crux of the problem.
Luckily glass run channel, both upper and lower is still readily available-and they are not expensive. If it was me, I'd probably replace the upper and lower channel run, adjust the guides (if necessary), and then not have to deal with it again.
rockauto.com is one good source for both the UPPER glass run channel and the tailgate channel material.
This page shows the glass run channel options that they have for
all the Bronco's windows.
