I'm not a master organist. But when I learned to play organ, I used to write fingerings my own by trying different ways. (my organ teacher told me to do it. Sometimes I found his fingerings are too difficult for me, and I had to change. He had much bigger hands than mine.) It was a good practice and discipline. Now I don't need them, (and don't even remember which fingers I use most of the times) only some places I write them. Also, you could use lots of finger substitutions for legato playing. Do you have any organ teacher around to get some help? (maybe a few lessons could help.) Sorry, I cannot help much but just a few words of advice.

The "Nova Organi Harmonia" is one of the simplest organ accompaniments to chant that I have ever seen. This is due, in part, to its modality in the inner parts. The function of this is that only a couple of notes move at any given time, and the texture often dwindles to 2 or 3 voices.

Writing out fingerings is only a help at the very beginning. Repeated playing brings out the more comfortable fingerings for any person. In legato accompaniment to hymns, finger substitution plays an important role - lifting a finger to move to another note breaks the flow. These breaks can be useful, at times, for leading; but not so much for accompanying.

I've been playing for so long that I don't think about fingerings any longer. But your question has caused me to focus on what my fingers seem to do naturally.

1) Fingers 4 & 5 are almost strictly for the soprano in the RH and bass in the LH.
2) Fingers 1 & 2 (thumb = 1) are for the inner parts.
3) Finger 3 waits on call wherever needed, often it's idle.

I hope this helps some.

For writing, I suggest a sharp #2.5 pencil (if not #3) so that you can erase when you find something you like better, and then erase completely when you no longer the fingerings as guides. Have confidence - that time WILL come!