Re: Hindle clearance
I've had a similar problem (mid-pipe hitting swingarm) w/ an Akrapovic system on my previous bike. It was a simple fix really though it took me a while to arrive at it. Try putting some thin (add more if you need to) spacers between the exhaust hanger and subframe. That worked for me and might give you the extra few mm's clearance you're looking for. As for the other Hindle header issue I don't have any ideas.
There was a good thread on this here somewhere. It's all about "shake fitting" the exhaust. Essentially keep all the bolts loose and tighten everything down incrementally checking for clearance in all the tight spots as you go from the headers to the mid-pipe and finally the can.
Good luck and take your time.