Following Alvin's suggestion I also used silicone sealer and had the same experience as Woody. It was easy enough to clean off the glass but the stuff really stuck to the paint on the frames. It took a long time to get it off. Thankfully I only did one side at a time. On the second one I masked off all the at risk paint and it was pretty easy to clean up. I did the vent windows out of their frames or I probably would have gotten the sealer all over the new rubber seals too. There is a lot of extra room between the frame and the glass without the setting tape, some side to side but mostly front to back. I assembled my vent assemblies and measured exactly where the glass should sit to make the best seal with the rubber. Then I took them apart and siliconed the window in the frame, pulling them back the required amount. The method Alvin describes of using the entire assembly to lock the window in place sounds like a better solution if you can keep the excess silicone off the rubber parts.

Chuck