If you wanted to develop expert systems, I suppose you could make the software try to find the best compromises for a given piece. Have a word with Kevin how he usually does this stuff! I’d think a good approach would be to just give the user a few options to choose before doing a mechanical conversion.
Your software/notation of course doesn’t have the same limitations as a physical shamisen. For example, you could have negative fret positions (-1, -2 etc). The user would then manually adapt the tabs to make it playable. (Perhaps some of those options could be performed post conversion.)