I would think that some type of mass spectrographic process would be useful, as well. After separating the buckyballs through filtration, or chemically, using the differential weight of caged versus uncaged buckyballs would provide a fine discrimination between the molecules.
If standard mass spectroscopy is too high energy, chromatographic techniques should suffice.
A clear banding should be apparent for "rustyballs" and the spectral analysis would be definitive.
The biggest problem is to characterize the location of the Fe; sure, you might have a mass of 776.46 daltons, but where is that Fe? Magnetic moment would show the presence of Fe0; 13C NMR would show a shift - if the iron is on the inside, rattling around, then the shift would be uniform for all the C in the buckyball itself, but different than that of C60.