I had to drill both the Pro-Wheel replacement rim holes out for my TTR125. Go figure, the nipples that came with the kit were too big for the holes in the rim, but just barely.
My spokes fit the hubs well enough. The rear is a drum brake, so it's a bit different, but the front is a standard disc brake hub, just like a YZ85. It seems the butted ends of the spokes didn't seat completely flush like I thought they should, but they tightened up just fine and have withstood a fair amount of abuse since then. But, my opinion of their product is somewhat skeptical.
I'd be somewhat leary of drilling the hub holes out on a 250. Then again, if it's not much of an enlargement, spread out over the number of holes, the difference in overall strength may be negligible. If you're fast, and jump big, I'd probably not do it, but that's just me.