I realized this a bit later, but yeah for organ writing especially in the pedals, I should have probably just specified when to use an extra octave in the registration (probably by writing forte and piano or something like that). My point of using octaves versus a single note was primarily for dynamic control, so if expressive pedals exist, that would almost certainly be a superior alternative. However, for the manuals, due to occasional crossing of voices, I intended for the organist to play octaves (this crossing is most easily observed at measures 11 and 12).
This was mostly a software limitation, though I expect that most organists who tried to play it would choose a quieter registration for the majority of the piece.
I have an incomplete fugue here (google drive folder), but to be completely honest this piece works just fine by itself, and I have no idea how any successive movements are going to be able to adequately continue what this piece started. It was never really intended to be this long, but just ended up this way in the process of writing it.