Sorry to hear about window & flooding. If you are not familiar with this, under the luggage comp. (trunk; right side) is the locking control pump/security module, an electronic & pneumatic system, (if I described it correctly). Water in here is known to do damage, a priority problem over actual top operation. Fortunately I have not yet had to deal with this, lots of info here, (sorry I don't know how to do the links.) Where in SoCal are you?
I believe pizzaguy & GraphiteGhost are very knowledgeable on top issues. Please follow up with what you find and do, good luck.