Tighed1,

I had this problem and tried your method, but it didn't work for me. I think my window had separated too much already (and I probably just suck really bad at this kind of stuff).

What ended up working for me was pulling the window completely off, then putting 3M trim adhesive double sided tape all the way around the window. Then I put a bead of 3M super weather strip and gasket adhesive on the tape and stuck it back to the top. After a day I ran another bead on the inside and outside of the window where it meets the fabric (I didn't come up with this idea myself, I found this method on the Internet outside the forum).

I did this on July 4th weekend. I live in Texas and we've had lots of heat and a few monsoons since then. So far no leak and no separation (I've also put the top up and down about 10 times). Just wanted to put this out as another alternative. I think your method would have worked if mine hadn't come off so much already. I think the tape helped to hold it to the top while the adhesive did it's work.