OK, this evening I have been experimenting.
Failure 1
Firstly I borrowed a set of Shimano XT parallelogram brakes, if anything works these should. Unfortunately the brake pivots are not central to the wheel and the left hand side didn't have enough room so the pad hit the tyre.
Failure 2
I went back to the original brakes, oiled them all up and used the hole that gave most tension hoping that they would pull back and clear the wheel properly. There is a slight wobble in the wheel which I expect, it's a couple of mm so I expect that is normal. Now the setup, I set the calipers wide so that holding the brake lever to the bar only put light pressure on the rim. The problem was that when I release the pads hardly pulled back at all and the wheel wobble means both pads touch the rim in one revolution.
Conclusions:
1. The rear wheel isn't dished enough, the wheel was rebuilt by SJS who said they got the dishing as far over as possible but the design of the hub worked against them. I don't know what can be done here as we are a bit stuck with the design of hub, SJS drilled and put eyelets in mine and it is still not great. This is more of an inconvenience because I don't notice when riding and it only means I can't fit cantilever brakes.
2. The brake lever isn't well matched with the brake arms and the position of the brake hinges (if they were slightly lower then the pads would be a bit further up the lever and have more travel). I don't know what can be done here as I've shown that brake upgrades don't help, I guess we need some Wisper advice.
So after a couple of hours work I am back to square 1 but with new brake pads fitted.