Once the aluminum is bare and wire wheeled wipe it down with vinegar and dry it, the mild acid will remove any light oxidation in the "pores" of the metal, immediately apply JB weld, oxidation occurs quickly so do right away.
Sand down the jb weld with a dremel, orbital sander or by hand then apply self etching primer, now you apply filler over the etching primer to any remaining defects. Another couple of coats of etching primer and then refinish with primer filler, paint and clear.
I see there is a debate on the quality of filler, first its all the same base materials in different quantities, talc being one of the primary ingredients and that's the problem with polyester fillers.
Some are easier to sand, have fewer air bubbles but all will absorb moisture (including the so called metal fillers) as does one part primer fillers, the trick to long lasting repairs with fillers is to encapsulate it. If there is one step to successful rust repair this is it, we see it all the time a rust repair only lasting a short time before rust starts coming back through the paint in the form of bubbles, many times when you pop these water comes out and when you grind it down you see the repair patch is still in tact with no further rust through, what happened?
Once the panel was welded and patched it looked great so its all ground down and "bondo" applied. the repair is doomed to fail at this point. Any pin hole anywhere in the seam of the patch will now allow the filler to absorb moisture (even from the air) from behind and wick out under the paint.
A coat of epoxy like JB weld over the entire seam inside also if possible will ensure the filler remains dry. Sand the JB down its only to fill any sort of pin holes which almost always happens even if you cant see them when welding thin sheet metal.
Once the JB weld is sanded down apply a self etching primer to the whole area then apply the filler, you have now sealed the filler from behind. apply a good quality 2k epoxy primer then a poly primer over that to finish the job then paint. The filler is sealed from both sides and the repair will last a very long time.
Back when I first started we brazed a lot of panels and it was not as big an issue, we also used lead filler on some higher end cars. This worked great on thick sheet metal but today its very difficult, panel distortion and the dangers of working with lead are nothing for the DIY or even most pro's today have never been taught how to use lead and more important use it safely. Pick and file work is nothing on new cars the metal isn't thick enough so they don't teach it anymore either.
