As I re-read the first post, I wondered if the scollops were on the fretting surface, or underneath, where the fretboard makes contact with the instrument top. The latter is a fairly common design, the idea being the top would be able to vibrate more freely glued contact with the fretboard.
I have played guitars and banjos with scolloped fingerboards. The idea is they are faster and more easy to play because finger placement is less critical. There is also the idea that it is easier to bend notes.
Sometimes the metal frets are set flush to the top of the flat fingerboard, then the wood between the frets is scooped out.
I didn't care for them, but some people like them.
I am coming late to this discussion, but hope I can offer a little help.
First, I think it is important to clarify the language. "To transpose" means to change keys, that is, move a piece from, say, the key of F (F, G, A Bb, C, etc) to the key of D (D, E, F#, G, A, etc). What you are doing is transcribing and arranging.
Back when I was a college music major, one of the exercises we had in the first year of Harmony was to fill in the notes of of hymns, creating 4-part harmony, given only the melody (soprano) and bass parts. The interesting thing was there was often enough implied harmony that the inner ear would fill in the "missing" notes. The alto and tenor voices often weren't necessary.
If I were working on a project like yours, I would first try working with the outside voices (soprano and bass) first, then decide which, if any, of the other harmony notes you need for a musically pleasing sound.
