Good thing you're already down with removing the System-1m. Devices that have their own cabs and power don't belong in a case that's intended for things which don't have them. It also sneakily increases the cost of your System-1m, as you're now housing and powering it twice.
I've spent a hot minute here looking at this build, sorting out what bugs me about it. And then it hit me...that 303 sequencer. First of all, it takes up about 1/4th of the entire build. Second, it's sort of an anachronism...it's something from the period where there were no decent TB-303 emulations or reissues, and while the voicing had been sorted out by that point in time, the sequencer was still defying redesign. And third, it costs half a grand, which I suppose is cheap when compared to a $3k original Roland 303, but which is dumb as hell when you can get Cyclone Analogic's TT-303 mkii for $300-350 street, brand new. And yeah, it emulates the original device almost perfectly. It would make a lot more sense to me to outboard one of those, then have a suitable MIDI interface in a smaller build overall (maybe as small as 1 x 104, even) so that you can pass note data from the TT-303 to the modular. Want to filter it further? Then add a Doepfer A-119 for an input pre + envelope follower. And THIS way, you can build a more general-purpose modular that 1) costs less, 2) isn't so huge because of huge modules, and 3) dovetails nicely with anything laying around the studio, instead of being mission-specific.