I'll be using All Metal body filler for all major work on the truck. Unlike regular body filler which is primarily composed of talc and which can absorb moisture, the All Metal is made with aluminium and so resists water a lot better. The down side: its more work to sand and some say won't take paint as well. So I'll just overcoat it with a thin layer of regular filler before painting.
The bottom of the step. The replacement step has the holes that VW uses to anchor the plastic step pad. They are the problem source of moisture which caused all the rust in the first place, so I'm going to seal them and do away with the step pads completely.
I've just used some slugs from an electrical junction box to seal the holes. With a bit of shaping, the slugs were worked to conform to the curved surface a bit better. I tack welded them in place, then sealed the edges with JB weld and used the All Metal filler to fill the depression on the other side. Once they are in place, I'll spray some rubberized rockerguard in place of the step pad to provide a bit of grip and sound deadening.