I've been dealing with these wheels quite a bit lately, all the way form the 86-87 to the 04 stuff. The wheels from 88-on are dimensionally the same, even though the later units have 3 bearings and the older stuff only 2. The actual track that the brake caliper slides wouldn't suprise me that its different, no big deal get the right year caliper. The swing arm width I would question, kawi used 2 different wheel spacers a 20mm and a 22 mm, the 22 mm was used on the older stuff before they started adding the small plate to the inside of the swingarm.
I think I would look at your wonderfully extended swinarm, ensure that the legs are straight and pulled in, if they are welded there is a tendency to pull and that could be your issue, or maybe the sticks themselves are not on the same plane as a stocker. Please post a picture to better help understand what your looking at.
I've done several and they remain constant throughout the length using stock spacers for the newer style wheels. now when using the older stuff, they require custom spacers. The older hubs are a bit beefier in sprocket mounting area, but only have 1 bearing so they require some machining to be able to add bearings, may not need to do that for a 500 but I've been bending axles and breaking hubs so I'm going a different route, it's amazing what 170 hp and bolts will do.