I was looking into this a few months ago, since I have a similar situation. Whirlwind has nice multipin connectors available, but they're difficult to assemble. When I looked at having them make custom fanouts on multipin connectors, it was going to cost upwards of $1000. I believe ProCo also sells a multipin connector. A 56-pin Elco connector would also work for you, and you can probably buy them with the multicore already connected at the connector end.
I had two stereo, eight audio, and one MIDI cable to connect to my rack, aside from all of the interconnections. I'm really lazy and I already spent all of my money on gear and cables, so here's what I did: I assembled all of my drum machines and synthesizers together on a folding table with their power hooked up to a power strip and their syncs and other interconnections made, like a pedalboard. Then I hooked up individual cables from the various machines to the back of my rack, labeled them at the rack end, and wire tied all of the cables together into a loom. So when I break down, I just pull all of the plugs out of the back of the rack and put the loom on the table with the other gear for transport. This allows me to connect everything in about a minute, whereas it took more than twenty before, and it's not such a rat's nest anymore. I'm glad I did it this way, because I find myself creating a new routing paradigm before every gig, and the loom makes it easy to reconfigure.
Engineer, Music Man R&D
Ernie Ball, Inc.