I'm assuming that your old window clips are broken and are moving independant of the window.
I would suggest that you carefully use a few gobs of essex windshield urathane to fasten the windshield to whats left of the clips. Might be easier to do it with the window at the bottom of the track, just make sure you know that it the window will seat nicely at the top of the track.
The urathane is quite pricey, but its the best, stickiest, most flexible glue I know of. Be careful not to get it on anything else, and use a good pumice hand cleaner and disposable towels for cleanup. Water makes the stuff cure faster.