Ryan,
If you are not familiar with the conventions of music notation for the
organ in the place and at the time the composer lived, the best thing to
do is to consult with someone who is. Take the MS, or a printout of your
notesetting effort to an experienced organist, and get their opinions.
What seems confusing to you, might in fact be part of an intelligible
convention.
If you are preparing something that is to be published, this person
might also be able to give you registration suggestions to make your
material more usable for less experienced organists.
ns
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