I'd make sure all that flaky/bubbly rust is gone before applying waxoyl, POR 15, etc. It will be tough to get in there but spend some time on it and you'll get there. Even just using a flat head screw driver to scrape off will help a lot. Then go with some coarse sand paper or something. Spending a little time now will save a lot of time later.
'95 Soft Top
'89 Classic Tdi