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Are your axle spacers on correct sides, as stated above, and are the hubs on both wheels the same width? (measure through the hole). Was the throttle side fork pushed in touching the spacer prior to tightening the clamp bolts? Are the bearings the correct size and fully seated?
Moving the calipers in a bit (note "a bit"- like one washer ) can be done with stainless washers ("shims") placed between the forks and calipers but it shouldn't require that if all above is correct.
Quite often the thickness of the chrome is enough to cause this type of "issue". Especially if the rotors and the wheel are chrome. Assuming spacers are in the right place you could shim the caliper if it needs to move outward to center the rotors, take off the rotors and use a file on the mating surface for the wheel, or file a little chrome on the wheel. Did you clean the pistons in the brake caliper, or put new pads at the same time?
Have you opened the master cylinder? Bled the brakes? Not enough info to go on here really.
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