Dennis,
Get yourself some of the 1" wide Butyl Rubber double-sided tape which is made for mounting these
windows, and is also used by OEM's to install these. Any RV/Trailer Supply place should have it on the shelf, as it is a pretty common item. You're right, you don't want to use silicone sealant on these, (or pretty much anything else for that matter.)
Sorry to hear about your damage. That really sucks.
Greg