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I have a crossride rear wheel in a soul frame and it sits more to the driveside leaving not much clearance on that side of the chainstay. Is it just aquestion of adjusting the hub on the axle to move it to sit more to the non driveside? Also if I do this I think the disk caliper will allign more to centre as it is nearly all the way to the right in the adjustment slot (avid juicy5).
Adjusting your wheel alignment will have no affect on the disc rotor whatsover. Sounds like the wheel just needs dishing.
I've used Crossrides on my Soul and didn't notice anything different from other wheels I've used.