Use a closed cell foam weatherstrip, can usually get it 1/16, 1/8" thick.Closed cell is what you want

 

I had this problem when I installed my LRS windshield because it is not as thick as the OEM windshield. I used a piece of inner fairing trim seal (p/n 58311-96; ~$5.00) along the top of the inner fairing. The OEM part comes with adhesive in it and will stick to the edge of the fairing and stay in place when the front fairing and windshield are removed and reinstalled.