Either:
- Programatically gather a list of all samples used in the song
- Generate many modified .spc files, each of which mutes 1 sample via editing the BRR data.
Or
- Use a modified SPC700 emulator which you can tell to skip playing a specific sample ID.
Record the original song to .wav. And for each sample, record "the song with one sample muted", and take (original song - 1 sample muted), to isolate that 1 sample. If the result is not silent, you have isolated 1 instrument from the original song.
The results may not always be perfect, and will need manual labeling of instruments, or manually merging together multiple piano instruments. But I think this process will work.