Dave, I wish I could tell you what to do but I can't, I can only tell you what I did on my wildrod project, and I learned it from my buddy who sold their bodies when they where in Canada. He did not use the conventional "cat whiskers" or typical window molding just a small "U" shaped channel that has got a 1/8" gap and the legs are about 1/4" long, he had me roll up my windows and scribe the outside and inside fiberglass the same thickness as the center of the U molding and I took a die grinder with a twist lok 120 grit disk and rolled the window down and ground the door on the inside and outside to the scribed line and then took a continuous piece of the rubber mold and installed it inside and out with 3m weatherstrip adhesive. This finishes off the door nicely and fits snugly against the glass with no rattle and very snug, keep in mind early factory window channel wasn't very water proof on the bottom as the door always had a small drain hole to drain the water that went in on the outside. This is my first post with pics so maybe this will work??

Attachment 62949Attachment 62950Attachment 62951