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layout is difficult - it's personal and there are patch cables of all sizes.. so no need to worry about that - find something that works for you - it may take a few goes over a few months

personally if you want all the modules in this case I would get an even bigger case to start with (or at the very least keep the case you have too), as you could almost definitely do with another row - mostly for imo utilities for manipulating CV - plus the most important Make Noise module of all: Maths

I find this ratio is a good starting point:

sound sources < sound modifiers < modulation sources < utilities

because you can send the same sound source to multiple sound modifiers, you need a lot of modulation in order to support the sound modifiers and sources and you need plenty of utilities, for controlling, mixing, modifying and mult'ing with and without voltage control all the voltages running through the synthesizer - unless of course you want to 'perform' with the case - even then I prefer the use lots of modulation - adjust modulation and re-route it method of performance as opposed to the frenetic micro tweaking you often find on youtube

things that could be cut back - sequencing - there's a lot of sequencing in there for not that many voices - I would remove rene for now - keep it for case 2 or row 3 or whatever - and I'd probably think long and hard about replacing one or all of the make noise effects modules and beads with smaller modules that will do similar things in less space - 2 or 3 fx aid xls and optionally a disting ex will give you something similar but take up about a third the space - leaving room for more utilities - or just use the old case

the major shortage I think is mixing - yes there are quite a few mixers in there already, but I'd want a matrix mixer in there - mostly for mixing modulation sources - possibly more vcas and definitely more filters and a wave folder

I'd also look at upgrading mixup as an end of chain mixer - you have x number of audio outs from modules and x-y mixer channels - and think about the difference between mono and stereo and how you deal with that/need to be able to mix mono (panning/stereo-izaton) and stereo sources together etc