'98-'03 R1's used 298mm rotors - close enough that you could get away with the VFR's 296mm rotors.
'04 -'06 R1's have 320mm rotors, while '07 models will have 310mm rotors.
If you have a set of forks from an '04-'06 R1 you get radial calipers. I don't specifically know if a VFR wheel will work, but that you can put Ducati 320mm rotors on a VFR wheel....so if the spacing were to work out that might be an option.
Limited sales of RC's combined with higher-than-normal attrition on the road and on the track is my guess. After awhile the used parts market thins out. Speedzilla's Sport Twins Classifieds can be a good source of parts sometimes.
I had a very hard time finding a replacement Ducati rear caliper this summer, and wound up paying nearly $50 for a part I bought a year earlier for $10.
Parts can be scarce due to lots of things - in the summer people are busy riding and perhaps not listing what they have for sale; in the fall what is available goes fast as people buy what they want for winter projects. Right now parts are relatively cheap if you can find them as people are spending all their money on Christmas. This will continue until the end of January, after which prices will rise again until about April. Then everyone will be off riding again and so forth.