Can you try another complete wheel from another bike ,at least that would isolate whether it's a problem with disc/wheel combination or the caliper.

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2001 X1 2009 1125CR 2006 Uly X3 2010 Uly a fully Maz'd S1 and a 1991 RS1200 Westwind.

I have one you can try...

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08 Specialized Langster

Not had the opportunity to look at the brake problem recently - will need to pull my finger out in the next couple of weeks though - but I also have a few mods to do to the V Rod.

Luckily I have a second 1125 - I had already considered swapping wheels to pinpoint where the problem lies ...