My 68SS is missing some of the little buttons that the molding clips mount to. They seem to be just welded on, but some are gone. How can I replace the molding clips and mount them to the window frame?

Any auto glass place can replace those missing clip studs. Generally though, it requires removal of the window.
FYI,I had a mobile glass guy do the rear window on my '80 Camaro recently...charged $100 to R&R the window and replace about 6 studs. Also included a new weatherseal. I believe they use small screws to retain the molding clips.

By the way...when I replace the clips, shouold I put the clips on after the install of the vinyl top, or before? I noticed that when I removed the old clips, the vinyl top material was behind them.

I just had my top put on my 69SS a few weeks ago. I had to replace the right quarter so the original rivits were gone on the quarter for the trim and at the right side of the rear window for its trim. Any glass guy can rivot in your window trim plugs, my guy says a sheet metal screw will also do the trick. The vinyl top guy didnt care if the glass was in or out. I sent the car to him with no glass. He called them T-nuts..but thats what he used on the right side outer quarter for the vinyl top trim. My glass hasnt gone it yet...naturally I am running into the same problem now that everyone encounters...suddenly my rsto man is busy with too much crash work from the local dealer and the car is starting to sit more often! Sound familar guys?