under the vinyl

I just took the vinyl top off my 66 coupe and it is solid rust and the metal is really pitted. What can I do to save some $ before I take it to the body shop to have the holes patched? (Sand, etc) Should I just sand off all of the rust and hit it with primer? It is pretty solid in some spots and real thin in others, as I said there is even some spots where it has rusted all the way through which I need to have a body guy patch. I am not going to put a vinyl top on when I'm done.

Thanks,
Brian