It's a lot of fun to listen to this piece--the organ is truly the king of instruments, as Mozart himself claimed!
I really enjoyed the passage from m. 54 to m. 61. It was wonderful (albeit a bit familiar) harmonic progression that built a lot of tension before landing on that big G Major chord. However, the section from m. 62 to m. 69 kind of just reused that same progression and ended with the exact same cadence, and I feel like the repetition didn't really add much to the music. A big half cadence like that suggests to me that something impressive and new is coming up--a passage of brilliant virtuosity (maybe some fancy footwork) or of great contrast, like the softer section that comes next.
As for where you go next, I suggest drawing inspiration from Beethoven's Grosse Fuge:
Beethoven begins with a similar structure--an introduction, a polyphonic fugal passage, and then a softer B section. He transitions out of the B section by reintroducing an ominous theme from the introduction, completely out of context. I think you can do the same thing here, even if you have to fragment an earlier theme and just use part of it as a short motif while maintaining your more peaceful atmosphere. I would choose a theme from your fugue, as you've developed that the most and it'll probably sound familiar to the audience's ears.
I hope this helped, and I look forward to hearing this piece in its completed form!
J Shu