You shouldn't have to remove the windshield to seal it. The Permatex stuff is just silicon rubber, packaged as some magical sealant. Personally I would avoid it.
I used the 3M weather strip adhesive, the black stuff. I just lifted the edge and let it flow in. The excess can be cleaned off with varsol, even after it is dry. I only sealed between the glass and the rubber but the corners really needed it. I don't have leaks now.
