I just had both my back side window panes out of my 76 Trillium
for tinting. Yes, the top ones did not want to come out. I had to ease (bend) the aluminum drip edge of the upper frame up, at one end, in order to gain enough clearance. I did the back top corner of each window. I used vice grips and two little pieces of metal to minimize the damage to the aluminum. I only had to ease (bend) it up about 1/4 of an inch and then I was able to wriggle the window past the rock hard seals.
(NOTE - You must be careful not to bend too fat as you might break the aluminum drip edge. Once you get the window out, you can ease (bend) the aluminum back into place so that it is hardly noticeable. )
Once the upper frame for the top glass was out I could clearly see what the problem was. The upper frame piece for the top glass is a little too long on both ends. It does not need to extend 1/4 inch past the side glass aluminum channels. I just used a dremel to shorten them up a bit. It's easy to play with this once the glass is out and you reassemble the frame. GET NEW RUBBER
from the glass company. They should have it. It makes putting the glass in the frame 1000 times easier. You could get the glass company to put the glass in the frame for you but then fitment of the frame to the window is harder when the glass in in. I hope this kind of makes sense. I do not claim to be an expert and I would not want you to damage your trailer. This is how I did it.
As far as the rock guard goes, if it's the piece I think it is I found that U-channel for the sides of the rock guard at Home Depot. It's not exact but it worked.