There are some big gaps in that weatherstrip. It will need to be replaced. Do you want to replace it on new paint, or paint up to the newly replaced weatherstrip? I was in the same dilemma. My build took years and I'm happy to have installed new weatherstrip on new paint. You could glop sealant into the gaps and around the perimeter of the windshield for now. The stainless trim should be able to be cleaned of adhesive in the future, it will be extra work.
