On the SR500 wheel I used on my bike, the sprocket side projects further from center than the rotor side. Sorry, I don't know exactly how much.
I centered the rear wheel in the bike by putting the frame on a stand and making sure it was level side to side, Harbor Freight sells a digital level for ~$30 that was invaluable in getting that part done. I then tied a string to the steering neck, making sure it had a 'V' in the loop so it would self center and ran it to the rear of the bike, draping it over the fender hoop. I put a plumb bob on that end to keep it taut. I then used a very long 6mm thread bolt in the rear fuel tank mount which was maybe 1/8" under my string and moved the string until it was centered over that bolt. That gave me the frame centerline. I measured the rim width and marked it with a center punch so I'd know the exact centerline, put the wheel on the axle, then put it under the plumb bob and slid it side to side till it was centered, then took my measurements. I had to turn .400 (almost exactly 7/16") off of the sprocket side spacer and then make a similar spacer for the rotor side to keep things centered (basically scooted the wheel .400 to the left). Once the wheel was centered, the sprockets lined up perfectly.