12 years ago I also had the same problem with the passenger side window. I had tried to fix it in the vice but I hadn't made it. In my Morgan workshop they had the solution, simply in seconds and permanently.
The mechanic had quite simply held the opened door and bent with his upper body over the whole surface the side window. I was very impressed but I wouldn't dare to do it myself. Sometimes the simple solutions are the best.
Now I have the same problem with the 4/4 for some time. And it is like with Keith. The side windows sit too far back and don't fit under the rubber guide which wasn't there in the first case I just described. Let's see I let the workshop fix it again.