I was talking to the bodyshop owner today and he told me that the surface rust on the roof could comeback to bite me in the ass, he advised that I get rid of it completely and not just seal it up. I tried pretty much everything, sanding it wire wheeling it, I finally tried some muriatic acid and it seems to be doing the trick, its slow however it might take few days for the rust to be completely gone.
this is what I started with a couple weeks ago.
I soaked some paper towels to keep the acid from dripping off
finally blocked the rest of the roof today. I have to go back over everything with 80 grit to get it ready for primer, and fill in a couple pin holes and such.