I wouldn't take the chance of using sandpaper next to/on top of clearcoated paint, even if tape was protecting it. I'd also be worried about overspray, unless you get large rolls of paper and protect one entire side of the car at a time. It's easy enough on a Saturday morning or something to tear down the rear interior quarter panels and remove the nuts holding the window in place.
You guys worry too much. Tape it off well; use a few layers if your worried about sanding through...then mask it off and paint. Pretty easy. Over spray wont be a big deal. No need to mask off an entire side.
I'm going to try the rubber trim restore product from this site.
You brush and sand so no overspray worries. I talked to him on the phone and says it would be great for any rubber moulding. I ordered it so I'll report when it's done.
classictrimcoat.com/
I am interested to see how that rubber stuff works out too. I have refurbished my quarter windows while still on th car and it worked great but could use it again.
Some 3M windshield eurathane works great too. I used some to rebuild the carb boots on my Mach Z last winter. It's dries hard, yet remains flexible when applied. Just block sand down the high spots, and add paint afterwards. Good as new.