Dave I was simply taking the OP's word as to the condition:

I have a very rusty absinth yellow HX van that's on the list of things to do. It has windows cut in the sides and a sunroof has been cut in. The roof along the gutter rail seems OK, the seam between the top and bottom is very ordinary and the sills and rear quarters are stuffed. Come to think of it the beaver panel is like Swiss cheese too. I have a really clean and practically rust free windowless WB shell sitting in the shed so my question is what would you guys do? If I repair the rusty Sandman it will always be a repaired Sandman and with the seam around the top/bottom rusty I imagine that would be a huge job to fix properly.

If I was to describe a car in that detail, to me the shell is shagged. And there is no point spending bulk $ and/or time on a car that has had a body swap. You can never advertise it for sale as an original Sandman given the recent court case precedents set with the rebodied GT, and as soon as you fess up it has had a body swap you can halve the value. Some people will not care, but the best return will always come from a car with reasonable provenance. For those that think with blinkers on, I think it is extremely foolish for anyone to take the attitude "i'll never sell it", you should always keep in mind what you are spending hard earned $ on, and knowingly pouring wads of $ into a rebodied collectable car is to me a big folly. Nothing wrong with having one if you pick it up cheap and limit your spend on it.
Hence my suggestion to sell it as their are people out their that pay stupid $ for rust buckets. Sandmans aren't rare, like GTR's and SLR's and GTS sedans there were thousands made and plenty are still around. You can pick up quality Sandmans for $20k, but you usually only ever see them advertised once someone out for a buck $ finds them and trys to onsell them for an easy $5-$10k profit.

I totally agree that you can limit your rust repair expenses if you do it yourself, but having seen the hours that can go into doing a body up to ready for paint if you have to pay someone for even half that you are going to be up there in $.