Is there an adjustment for the windows so that they seal better against the rubber when the top is up? and against each other? I have relatively new rubber but the windows still have a substantial gap between each other and the top. Is this what the door wedges are for? any help will be appreciated.

You need to get the service manual "Body by Fisher." It goes into great detail concerning window adjustments. Also, shows how to adjust the top if necessary.

for sure get the manual, there are lots and lots of adjustments....