Thanks for taking the time to give it some thought chaps.
Ross, I have had each piston all the way up and down their travel, but with my apparently, closed circuit system, one comes out as the other goes in....No I haven't had it apart, I would never do so unless I had planned a complete re-build with new seals at the ready.
Utopia, I will try and look at alignment when the new bushes and pads arrive, but rather difficult to actually check in reality. There is nothing to adjust in any way. It goes together as is and that's that.
Wheel alignment cannot effect calliper/disc alignment either, as they are common to the wheel spindle, in the case of both floating and non floating set ups.
It is possible that my calliper bracket is twisted? this was brand new from Ducati only about 4/5000 miles ago ( the powder coaters lost my original). The middle bush, pads and torque rod ends were all changed at the same time....And yes I cleaned all the powder coat from all critical areas.
I think the master may have been sealed or restricted from the res for some time. Maybe I only just managed to get the pistons back enough when fitting the new pads? The pads have sometimes shown signs of dragging a bit, sometimes clicking in the calliper when turning the wheel so perhaps they have been tight enough to wear in the wedge shape and also load the bush enough to cause problems there too.
The irony is that it seems to be working really well assembled back dry, with the pads nice and clear of the disc. But I don't have the balls to take it back to the tester without really addressing the problem...Knowing my luck the pistons would move out properly on the journey there and bring back the hill start wheel syndrome again.
Looks like the master will have to come apart...I hate messing with hydraulics!!