I have been using a program called Harmony Assistant by Myriad Software
to adapt MIDI music for my John Smith organ.  It is a music editing
program similar to Cakewalk, but I personally prefer it over Cakewalk
for ease of use.

What I like most about this program is that you can define the notes
available for a particular organ (called a filter in the program) and
then have all notes in a particular MIDI piece colored red to identify
them as not available.  You can then manually adjust them (or optionally
delete them all).  It also has the ability to print a music roll for
punching, which Cakewalk can't do.

The only problem I have is that it can not handle the unequal hole
spacing of the John Smith busker.  I wrote and asked them to add this
feature but they said that not enough users had asked for that function,
so maybe if enough John Smith busker organ users asked for it, they may
include it in a future version.

By the way, the program is very reasonably priced.

Kevin Oliver