Good to know about the reason for the 1Mhz maxfreq...
Not really sure what to do with the viola d'amore source sounds if they are just not going to be stable.
I think if you can settle for fewer harmonics and work out the flag logic there's hope yet. Another thing that occurred to me is that since the scratchy noise part of the viol sound is likely what's making the tracking jumpy, you could try to remove the noise. I've been working on an external that lets you rescale the amplitudes of harmonics in a pitched signal. There's an early draft on my website - it's called [pitchEnv~]. Using that, I scaled all the harmonics of your sample to 0, so that all the pitch related components are erased from the signal. The attached wav file is what's left...basically all the scratchy noise.
Then I tried subtracting that noise from the original signal (delayed slightly based on the time it takes to do this analysis), and it did clean up the noise some. It wasn't perfect, but with some work this could produce a signal you send to [sigmund~] that would be more easily tracked out. I might have time to fiddle with that later, but if you download [pitchEnv~] you can give it a shot too.
William