I used locktite brand of adhesive caulking. I don't remember for sure exactly which one. I used it when I reskinned the windows. Seems to be working good and no leaks. Still alittle flexable. Its been almost two years and 4000 miles. Got it at lowes.
I am going to rivet (more of them) and then drop in the windows which will probably need some square tubing and more rivets and will then pack the open areas where the windows were with polyiso sheet insulation then fir them out.