OK, I checked it out. Other than slight cosmetic differences, the only difference between early and late hubs is the counterbored bolt holes for clearance for the shoulder bolts. It should be easy to counterbore the bolt holes in the early hubs to accept the late shoulder bolts. It would be best to do it in a drill press. In the pics below, the early parts are always on the right side of the pic. Ideally, you need a letter size X drill bit(.397"). If you can't find one, a 13/32" bit(.406") should be OK. The shoulder on the bolts is .010" smaller than the counterbored hole in the hubs, so I really don't think the counterbored hole has anything to do with the function of the bolts. Counterbore the holes 3/16" deep. It really only needs about 1/8", Yamaha did it 3/16" and you want to make sure the shoulder doesn't bottom out in the hole. Just don't drill too deep as you start losing threads. When you get the late style bolts and rotors in your hand, you will see what I am talking about.
If you slightly grind a flat on the cutting edge of the drill bit, it won't dive in and spin the hub around on the drill press table. The last pic shows what I mean. This is for drilling soft metals, especially in cases where you are drilling all the way through.