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Man, I wish I could help here. This is a great thought exercise, but I feel like once a rack reaches a certain size, the arrangement all depends on highly personal choices and workflow.
Personally, I'll be maxed out on space at 832hp soon, and had to make some recent arrangement choices that may be odd to some of the folks here but make perfect sense to me based on how I use the thing. I really just looked at what I wasn't using and asked myself why. If it was because the module didn't fit into the concept/sound I was going for or if I hated the interface, I pulled it completely out of the rack (goodbye Clouds and Phonogene) and opened up that space for something more practical. No use for me to eat up time and space with something that is just not working. If I wasn't using a module because of where it was placed in the rack, I moved it closer to the modules I use most often. That was actually the case with Maths for me. I wasn't getting the most out of it, but now I use it all the time simply because I moved it closer to where I have my hands most often.
I have spent way too much time scratching my head, configuring, and reconfiguring my rack here on MG before making any real-world changes, all the while being mindful of how I actually work (which is probably way different than your approach). Then I finally took a few hours on a Sunday and actually completed the "Great Rearrangement", but I still spent time over the next few weeks moving a few modules. Now, I'm really happy with my arrangement, and getting the most use out of everything.
I think if you follow the general guidelines we've all offered to the novices here (e.g. maintain a sensible signal flow similar to a hardwired synth architecture: osc -> filter -> modulator -> vca -> effects, keep similar module functions together or separate them out into multiple voices, etc.) but on a larger scale, it still applies. But give yourself an allowance for having certain modules in seemingly odd places because that's where it makes sense for you.
Have fun with it. I wish you luck!