I'm in the same process right now. I've got the sr500 wheel and a xs400 wheel. The GIANT cush drive on the sr500 convinced me that the easier solution was to go with the 400 since the smallest sprocket I could find for the 500 wheel was something like 40 tooth. I thought that the rd400 wheels were the same (as the xs400), but I don't see any shape difference like 1974jh5 mentions, and the sprocket options are a lot closer.
I haven't solved all the problems yet, but the most significant seem to be the offset between the sprockets which by my measurements is 1/4". I've read some threads that suggest it is 3/8 per side, but it looks more like a 1/4 on the sprocket side and 1/2 on the disc side to me. By switching to 520 chain and sprockets and turning the offsets toward each other I can cut that 1/4 down to 1/8, so I see no need for a spacer on the sprocket side.
I'm thinking that I may run a different caliper, so that side I haven't worked out yet. The 400 has a 5mm disc, so that opens up a lot of options, but the bolt pattern is the same, so I could use the 7mm 650 disc as well. I'd prefer to use the lighter disc and a lighter caliper as well. My 500 wheel has the 5mm disc as well.
I can get bearings with the 400 od for the 20mm 650 axle, so that isn't a problem. Google will get me dust seals that will work with whatever axle spacer I use, I'm still not 100% what I'll use for those spacers, but I may just drill some round stock with a 20mm hole. The 500 wheel also has the 17mm axles, so this problem would have to be worked out as well.
Sorry for the wordy post, but I've spent the last week wrapping my head around this problem and I might as well share.