It could be a case of adjustment. You have in/ out, for/aft, up/down adjustments, and you have these ajustment points at the fron and back of the door glasses.
This can create an incredible mess. Sometimes, adjusting either the q/g or the d/g requires adjustment to the adjacnet glass.
Adjustment is a skill, and unless do it, or have done it professionally, you just have to keep dinking with it. Even professionals have to dink with them.
I don't know if you have priced new glass for your car, but it's a real horse pill to swallow. (There are a lot of cars around that if the glass were broken out, the car would be totaled because replacment glass exceeds the value of the car.)
I won't try to influence you as to whether or not you want to buy new glass. One thing I'll point, out, however, is that you might want to play around with the adjustments before you go out and buy new everything as to related components.
It's impossible to try to even start to explain how to adjust glass. Hell, most glassmen don't know how to adjust glass.
Let's say that I had a stripped door with parts that didn't have telltale scars as to where everything lines up. This is how I would get my baseline adjustment, then dink with it if it needed more: Install the glass without really tightening everything up. While inside the car with the panels removed, I'd roll the glass up coaxing it into basic alignment, weaseling it around, getting it into the hole the best.
Then I would snug everything up. I would get out of the car, AND GENTLY CLOSE THE DOOR. AGAIN, GENTLY CLOSE THE DOOR, checking the alignment. You close it gently because if it's major cadywampus, and you give the door a hard slam, the glass's edge may catch an edge. Oh, yes, it could go BOOM! and you your glass could end up as clear gravel.