While it would be a major PITA, taking the top (skin only) and the offending window to a good luggage repair shop might work. I have had our local one repair five foot zippers on expensive, leather musical instrument gig bags. The bags cost me like $700 and are huge and heavy and awkward to work with. The guy was able to repair one zipper in place and replace the other one completely. The replacement would probably cost you like $200 or so.
Call first, as they might not want to do it, but honestly, the rear window zipper is *easy* compared to the expensive leather bags I gave my guy to fix. These shops are generally set up with YYK zipper machines to replace them on large suitcases. The rear window zipper is not much different than one of those, though we use the larger-toothed zippers.
Alternatively, you could call Bestop and see if they will replace the zipper if you pay shipping both ways. That, too, could save you some big bucks if they will do it. Just remember, they make their money by selling you new stuff, not fixing your old stuff.