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Its a weird one alright.
I haven't studied the master cylinder design closely or stripped one down to have a look but the over-retraction of the pistons does sound like the reservoir is isolated somehow and the pistons are therefore being sucked back.
I'm not familiar with the fine detail of the floating rear brake set-up either, but I would be inclined to check that everything lines up laterally like it should (once the play in the bushes has been eliminated).
When I was fitting the ally swingarm I assembled everything but left the pads out of the caliper. Its easy then to see if the disc is sitting central in the caliper body.
I guess I'd be checking wheel alignment too, but I can't really see that being far enough out to cause sufficient misalignment at the disc ... not that I would expect such error on your bike anyway, but when you're clutching at straws they all look worth grabbing.
Not a huge amount of help there I suppose ... but I'll be pondering.
I can't help thinking that its less likely that both the "won't turn backwards" and "sucked pistons" are two independent faults occurring coincidentally .. more likely that the two faults are somehow related.
BUT I can't see the link at all .. yet.
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