I am glad to report that I had some silicon spray in the garage, long since forgotten - and there was no need to bring in the nuclear weapon of KY. But the silicon worked great, especially on the driver side where I sprayed the heck out of both track and seal. It was a little tougher on the other side for some reason. On both sides, I was worried the whole time that the new seals would tear because I had to put my weight on them to get them to go past half way. I did not want to destroy brand new, fairly expensive seals (I got them at the Detroit Muscle Technologies booth at the Carlisle PA Mopar show in July). But they held up.
Check out the photos. You can see, if you look close, that on both sides there is a slight gap, maybe 1/8 in, between the top of the stainless track and the top of the window that the rubber seal does not cover. In both cases, the seal is down tight against the upper edge of the quarter window glass, so I am not sure what is causing this. Either the stainless track slipped down a bit along the glass, which is hard to believe, or the rubber seal top is not quite tall enough. I can slip some extra rubber material in there to close it.
The door windows both need adjusting, especially on the passenger side, which will be a project to tackle soon.
Also, just an FYI, I removed the driver side roof rail and rubber seal temporarily so I could adjust a couple of things. Years ago, I bought two used roof rail seals at a Carlisle show for $20; they were in mint condition. I used them last year when I put the roof rails in after the vinyl top went on; now I can't find the driver side seal anywhere in my garage! This is what happens when something becomes a lower priority and months go by... grrrr - a new pair is around a hundred bucks. The thing is around 5 feel long too, kind of hard to misplace.