I am almost finished with my soft top window top project. I completely stripped them down, re-painted them (Portofino Red) and have installed the Garrison Outfitters EPDM window channels http://www.garrisonoutfitters.com/ProductPage1.html
If anyone is interested, I would be glad to share my experience and some tips.
The Garrison kit is very complete and the instructions are pretty good. The key, as I found out, is to really get the channels absolutely clean of debris from age and the residual glue/fibers from the old felt.