I’ve also been thinking about doing something like this, here’s a couple of thoughts.
If you break apart the MIDI connector and insert the pins in the socket individually, rather than using permanent epoxy, I’d use E-6000, which is a good silicon adhesive that sticks to almost everything but it doesn’t dry out. Years later you can unpeel the silicon and remove/replace the cable. I’ve found it at Ace Hardware and Hobby Lobby.
You could bring the MIDI in via the USB connector. According to the latest rev of the ModFactor manual, v5.2.0[6] p.33 : “ModFactor automatically selects either USB or DIN5 as MIDI Inputs and Outputs. If USB is connected, DIN5 MIDI activity (including MIDI thru) is ignored.” But if your setup is otherwise all MIDI, you’d need a MIDI-to-USB converter.
But, the MIDI association has defined an official specification for MIDI over small phone connector:
They also recommend using one of the extra small 2.5mm connectors instead of the 1/8″ size. Those are definately available in a lo-profile right-angle type and it would only require drilling a very small hole in the case and soldering three wires.
{Note that the source and sink are reversed from that shown in a previous post}
