xelaris wrote:...and in fact, I've applied some rust converter (very expensive stuff) for a nice clean job in the differential and other bits - that was really bad looking but the first garage didn't fail the MOT for rust under the van which looks a lot better now than last year.
This might be where the problem lies... rust converter won't convert rust back to good metal. It might look cleaner and less rusty, but IME MOT testers don't worry about visible surface rust anyway, they're looking for rust that's penetrated enough to affect the structure. So while it might look prettier now, if he can still stick a screwdriver through the scabby bits that's still a fail. The only real solution is cutting it out and welding in new metal.
To answer your other question, yes you can totally do your own welding for MOT work. As long as it's up to standard (seam welded all the way around etc... look up the rules and requirements) it's all good. I've done some fairly extensive welding on my wife's car after the MOT guy found a hole he could put his fist through in one of the strut towers

and he was happy with the result.
You can get a cheap welder and all the gear you need for probably less than what a decent welder would charge for a simple patch repair, so it's a good investment.