You can interpolate FFTs also, and you can often use the higher harmonics for increased precision. You need to know a little bit about the harmonics of the instrument that was produced, and it's easier if you can assume you're less than half an octave off target, but even in the absence of that, the fundamental frequency is usually much stronger than the first subharmonic, and is not that far below the primary harmonic. A simple heuristic should let you pick the fundamental frequency.
I doubt that the autocorrelation method will work all that robustly across instruments, but you should get a series of self-similarity scores that is highest when you're offset by one fundamental frequency. If you go two, you should get the same score again (to within noise and differential damping of the different harmonics).
