The stock XS 650 rear wheel is a 16 incher and the sprocket bolt pattern is rather large (6 bolt-the sprocket is kinda like a sprocket ring).
The RD's and XS 400/500 (and others) use an 18 inch wheel and the sprocket bolt pattern is on the same bolt circle ( but 4 bolt) and would probably be a better wheel to start with. Using the RD/XS 500 rear wheel with require the bearings to be changed to 20mm. Personally I would use the XS 500 wheel as it has the spokes machined for more caliper clearance (the spokes on the RD wheel are "flat", where the spokes on the XS 500 wheel are dished).
1) RD wheel (spokes are "flat"). It shows the size of the sprocket/ sprocket bolt pattern also.
2) XS 400/500 Rear wheel. The spokes have extra machining to give them the dished look (the stock XS 650 wheels are like this also). This extra maching gives more clearance for different calipers.