I had a different take on this. Since much of the architecture of the original build depended on normal-sized Mutable modules (or around that same general size), I opted to yank them and replace them with smaller clone versions. This freed up quite a bit of space, as you could imagine...
So, when you examine this, you'll notice that nothing was really removed as such...but the additional space in the top row allowed me to add a noise/random source, a second oscillator (the Knit, clone of Plaits), a waveshaper that can also crossmodulate signals from both oscillators AND which also gives you an suboctave source. Nanorings, your multimode, then a Monsoon, which is an expanded version of Clouds, ONE, stereo mixer, then Verb. This also puts all of the audio (save for the output module, which I kept here) in the top, modulation and control in the bottom.
And in that bottom row, I went off...first tiny thing there is one of Konstant Labs' PWRcheckr modules, lets you keep an eye on your DC rail behavior. Then I tossed the old Doepfer divider and dropped in a six-way clock divider/logic/multiplier to really punch up your timing control. Sequential switch next, then a dual CVable Boolean logic module for further messing around with timing behavior (plus, Boolean gates can also make for nifty waveshapers in their own right). Then we're back on track all the way down to the Batumi, which now has its Poti expander. ADSR after that, then I shrunk the Veils down to a Codex Modulex clone in 8 hp. Disting's next, then the output module which now has more to deal with, so yeah...it makes more sense now.
Sure, this is a massive reworking, and it does require a number of module swaps. But it also massively expands the timbral and timing capabilities. And in this case, I kept the original cab size...but it strikes me that you might actually do better by first expanding the cab itself to a dual 104 hp, which would allow you to keep much of the original Mutables AND also allow for the expansion. You might even consider one of Intellijel's cabs with the extra 1U (Intellijel format) tile row for additional functionality.