This is a mind-boggling subject, but I'd like to throw in my ideas on
it.  With music box cylinders it's fairly easy to tell how many "lines"
there are for each cylinder, as they are almost universally scribed
with these lines.  There is also usually intact a tune-changing snail
which indicates the number of tunes.

Most combs that I've seen have the lowest three notes in a major chord
(i.e., F-A-C), so there's the next point to start.  In terms of trills,
here we start to get into trouble, but if the two adjacent notes are
commonly repeated in succession, it's likely that they are the same
note.

Many combs have scribes on the underside of the comb showing us the
tuning for each note and, to give a general rule, most of the notes are
repeated on the average of three times (but there are more exceptions
than the rule).  Organ pins in a music box are easily recognized by
their pin diameter and shape, but bells and drums cannot be
distinguished from regular notes.

I don't know how you are reading the pins, but if you are doing it
optically, you can start with a short focal length lens and fix the
focus exactly at the cylinder; this would avoid bent pins, etc.

Regards,
Eliyahu Shahar