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Said this before Ewan but you've got this wrong. You say the R/H side is aligned but it isn't. The inner brake pad is the one that needs to be perfectly flat with the disc not the outer one, you cannot really gauge whether it's in line without the caliper being in place, think of this logically, if the caliper were fitted as you have it the rear pad would sit at an angle to the disc, both pads would then wear at the same angle, you'd end up with crap brakes until they both wore to match the disc.
The 500 speedo drive plate is the one on the right, (in the pictures in reply #5) the dished one with the 2 ears
the 500 didn't have what appears to be a collar behind the speedo plate on Ewans picture (4th picture in reply #2), this appears to be extending down the spindle and looks at first glance to be part of the speedo drive plate, however after Ewan has posted the pic it's clear it's not so is this collar part of the speedo drive itself or something that Ewans fitted ?, don't think it's part of the spindle unless the angle the pic was taken at is confusing the issue.
As for the hub Ewan, yeah 9mm thinner would make sense as regards to where the discs are sitting in relation to the caliper arms, yeah if you could get the calipers perfectly aligned then it wouldn't matter BUT why go to all that trouble? replace the hub with a bog standard 500 hub and you'll get the L/H caliper perfectly aligned after and once you see how that should align it's a lot easier to visualise how the new R/H caliper needs to be mounted.
I think you've finally got what I was trying to point out, it's the inside caliper pad which because it's a fixed pad that needs to be perfectly flat to the disc, the outside movable pad then moves to take up the clearance. .
To adapt the original 500 speedo drive plate all you need to do is to grind off the dish part with the 2 ears on, go down to almost the flat part of the plate, I used valve grinding paste and a piece of glass to get the rest of the dish off and ensure it was perfectly level. All you do then is to fit it into the speedo drive, fit the spindle through it and then fit the spindle through the wheel bearings, that aligns the drive plate up with the hub, as you've cut off the ears you now need to ensure it's centrally located and this way does it. Hold the plate tight against the hub and remove the spindle and speedo drive, I then used 2 knock rivets out of an RD400 steering lock to hold it onto the hub, you'll need 2 holes drilling into the plate and hub and once it's properly aligned as above you secure the plate to the hub with the rivets. Quick spin of the wheel with the speedo drive in place and check to see everything is not oscillating and jobs done.
GL1000 disc bolts are ideal for mounting the twin discs as they are the correct length.
Are you sure the wheel bearing with screwed collar is all the way in to the shoulder as that would make a difference?