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Don't forget the brake plate is different as well, they will swap one way round but not the other as there is a difference on the outer diameter as well as the "Hump" the spindle goes through
I think about 50% of the bikes I own(ed), mostly the cb500 and 550s had some sort of gap issue on the rear wheel and swing arm but beyond bunging in the odd washer to keep it all alighned I have never let it bother me, often the swing arm flexes in a few mm when I tighten the rear spindle, as long as it ends up in line the bike handles fine, passes mot's etc, if fussed about the washers being unsightly, measure the spacers plus washers, get someone with a lathe to turn up a spacer the right length
Deltarider, try removing the rear bearing retainer on your wheel, the sprocket carrier is meant to have some grease on the surface where it meets the wheel boss, the reason for this is because as the dampers which cushion the sprocket carriers are crushed under acceleration etc the carrier itself moves very slightly forward, if there is no lubricant between the 2 surfaces you get wear, this could be where the metal dust is coming from, if there is enough wear the carrier will start to fluctuate and the sprocket will start to oscillate, meaning more chain wear and noise.
I presume you've still got the sprocket dish fitted?
If the bearing retainer isn't tight then you will get sprocket float as the entire cush drive is moving around, best get that sorted ASAP as the chain may come off if it gets to a certain point.