This would be interesting to know for sure... I continue to read that they are NOT interchangeable, but I don't know this for a fact.
I can certainly suspect the rear won't bolt right up, as the rear caliper mount is completely different between the two bikes, and thus has different spacers, caliper mount brackets, etc. The rear rotor is also 20mm larger than the Gen I rear rotor.
Similarly with the front wheel, it wouldn't be a direct swap without at least changing the rotors, since the Gen II bike has 310mm rotors, vice the 320mm rotors from earlier Busas. The change in brake caliper layout (radial, vs. side-mount on the Gen I bike) might also cause problems.