I'm going to throw my 2-1/2 cents worth in and if ends up that's only what it's worth, then so be it.
First off, I'll just say up front that the layout for the speakers you've come up with would not be the approach I'd take. Even though in my case one experiment involved a smaller number of speakers laid out in the same arrangement, the end results were not good. I feel it's was for 2 main reasons. First, yes when you only have a limited number of stops pulled, as you notice it sounds good, and it should no matter the speaker layout and it's mainly because you don't have several speakers competing with each other. However as you notice, things go down hill so to speak as you pile on the stops, which leads me to my second reason. I feel the issue is the speakers are all too close to each other which first, blows the sound-field regardless if it's stereo or mono, the speakers are simply just too close to each other. I've tested speakers directly alongside each other and also with some space in between them, and as I've noted several times in some of my testing and reports here, speaker positioning alone by a few feet can make a HUGE difference in the sound outcome. Playing into this issue is you are likely using the cyclic option which as you know ends up with sound coming from all over the place and you have zero control over this which I feel presents a problem in itself. I have to be honest, from day one I have not been sold on the cyclic options, this idea on paper sounds good, but doesn't make sense to me because of some of the issues you encounter that I lay out above.
Next, I feel it's imperative that you treat any speaker layout for an organ in terms of either by divisions which works pretty good, OR better yet by stop pitch. You have to look at it in terms that an organ is broken up into many small families of stops or pipes. A given rank of pipes are not thrown all over the place inside the organ case, they're in a group together somewhere in that case. So, when it comes to speakers, why treat those same pipes as if they are all over inside the case in random places by having them sounding on random speakers all over the place?
If it were me, I'd take your 24 channels per side and arrange each side in most likely a total of 6 groups of 4 speakers each. In addition, regardless of the stop, each stop needs equal representation, so hence my feeling for equal representation is you need an equal number of speakers representing each.
I would first lay out the speakers in columns of 4 stacked on top of each other, in this arrangement you end up with 6 stacks of 4 per side, the stacks I would say need to be at least a foot, probably more like two feet from each other, this you could experiment with some but I'd say this should work quite well. Any further spacing and things could go the wrong direction again.
Next, assign stops based on pitch per each group of speakers. Let's say your first stack L / R is channels 1-4, assign all stops 2' and higher including mixtures. Next for channels 5-8 L / R assign all 4' stops, channels 9-12 L / R all horn stops, channels 13-16 L / R all 8' stops, channels 17-20 L / R all 16' stops, leaving channels 21-24 L / R for any 32's, maybe odd ball 10-2/3rd stops, Prosaune, Bombarde, etc. Here again you can experiment some with a few stops to see where they fit best as you might find in this arrangement maybe the mixtures as an example play along nicer with the group you sent the horn stops to as an example. But regardless, you should not find in following this recipe that you need to re-invent the wheel in terms of where certain stops need to go, it should be pretty simple and I think you will be quite pleased with the results.
Oh, and just one more little add in here, the Armley Schulze would be an awesome choice for instruments.
Marc