The piece that holds the weather strip has a strip of thin foam between it and the roof. It is adjustable in and out and it is trial by fire to get it in the sweet spot. Is the glass adjusted properly? If so it will help get the position correct. What are you doing for the weather strip? Is it new or used? I believe Steel Rubber is the only proper fitting manufacturer. It should have a molded in bend where the roof angles. Mine wasn't Steel and had no bend. I cut the strip and rejoined it to get a better fit in the angled area. I think I installed the roof gutter stainless first, it's been several years. You should get more info from others on this site.
