68 Quarter window postiion

The quarter windows on my 68 have never worked really well. One had a broken roller. The other just needed some cleaning.

I have two challenges.

Challenge 1 - Window height
When the rollers aren’t in the tracks I can slide the windows all the way down the tracks to the stops. But when then the rollers are in the tracks, the window will stick up about an 1.5 inches above the chrome trim and the roller is at the end of the track. Should it be flush with the trim? Or, should it be above the trim.

Challenge 2 - Roller popping out of the track.
When I crank the window up and down a few times, the roller in the horizontal track will pop out towards the back of the car. It’s as if when it gets near the end of the track as I start cranking upwards, instead of moving forward in the track, the roller wants to move backwards first and then forward. What would be causing this reverse motion?

The factory shop manual goes into significant detail about how to adjust those windows. It sounds like you have a classic case of bad rollers, no lube on the tracks, and maybe typical rust on the tracks. You have to address all of those problems typically. The windows work great after all that.