First Off....Be absolutely sure that your roof is rust free...very often underneath a vinyl roof there is rust due to the vinyl trapping moisture. I would recommend that you strip the roof to bare metal...be cautious of your C pillar (the area between the roof and the rear quarter panel), this is where the factory joined the roof to the rear quarter and filled it with lead. If your using an abrasive like 80 grit on the DA make sure you cut into the lead seam as little as possible. If your roof is rust free using the SPI epoxy over the roof and then doing your body work is fine. If you have rust, repair the rusted areas, apply your Epoxy and finish your body work.
Hope this helps