[ApacheNick]

The only real fix is to cut out the bad spots and replace. Trying to weld up those holes will just make bigger holes because the metal will also be rusted away from the inside, most likely. Filling them with filler will also likely fail sooner rather than later because moisture can get to the filler from the back side allowing rust to start between the filler and the steel.

Assuming that is the worst of the rust holes, they do look like they'd be easy enough to make repair patches for though.

One other thought is that if this is going to be a temp. repair kind of thing, you could fill them with JB weld. JB weld is water proof and being an epoxy, it's kind of the same as your primer. I know it's kind of hack job sounding, but I have heard of this being done as a permanent repair for small rust holes and it seems to work well provided that all rust was removed.