Good news! The external mutes set a VCA state so it looks like it’s byebye relays. Thanks for the heads up - this should save a lot of work.
Very cool. ;D
Smash, please excuse the daft question but when you mention bypass caps on the +5/Ground lines,
hehe no such thing as a daft question, especially when you are talking about bypass voodoo. There are daft answers though, and I’ll do my best not to give you any… 
I think you mean in the MIDIbox (not the +5v logic supply on the console)?
correct
If so, where would be the best place in the circuit to add them? I’m guessing before / in place of C5 on the Core schematic?
This all depends on if you will be using the console logic supply or an separate supply…If your console supply is beefy enough to run the MIDIbox also, you will want to lose almost everything in the Core power section, and put that big cap across +5 and gnd as close to where the power comes in to the Core as possible. In other words, if this were my build I would lose J1, BR1, C5, C6, and IC3, Then I would bring in the 5v logic+gnd from the console on J2, and wire the big cap directly to the pads for J2.
Looking at the notes from the last broadcast meter bridge I built many years ago, on a clean linear supply one 10,000mfd @ 15v across the power rails, and the usual .01mfd caps everywhere were enough to keep the 500+ LED contraption from noising up the ground rail…the big cap is kind of an indirect way of lowering the noise floor, since a lot of self generated digital noise on the power rails it due to fast changes in current requirements vs. trace/path impedance. This is minimized by the cap helping the power supply meet demand from the circuit at the point of load.
The car stereo guys use the same technique these days, calling it a “stiffening” cap. 
Also what would be a realistic value for the smaller caps on each connector?
The usual .01 mfd should do fine, I would build it first, listen & test, then add these only if there is a noise issue.
If you do end up going with a separate supply, you might consider losing the ULN drivers, and driving optoisolators in place of the usual DOUT/LED configuration…This would keep everything isolated like the relay method, but without the relay coil noise. 
So I can get a little more specific…what is the make/model of the console? I’m hoping we can dig up a schematic and get a more accurate idea of what’s a good idea and what is a bad one… 
Best
Smash