Looks like an interesting project… I wish I had a vintage synth worthy of MIDIfication…
The main problem you have with this circuit is the keyboard switches are in a matrix.
At a guess, N2-N7 are outputs from IC1, one of these will be high, the rest low. When one is high, then any closed switches (pressed keys) connected to that output will conduct the high signal into B11,B12,B21,B22,B31,B32. You can view this as a group of six keys being “sampled” as each of the N2-N7 outputs is cycled. (Also, some other switches are sampled this way, like the waveform switch).
Now perhaps the easiest (but rather brute force) method of adding MIDI In would be to connect something like a 4066 chip, i.e. bilateral switches, in parallel with each switch of the keyboard, and then connecting the control pin to a DOUT pin, and running the MIDIIO128 application. The application should be easy to configure and not require any real coding to get things working. One 4066 chip could drive four keys. See here: http://www.fairchildsemi.com/ds/CD/CD4066BC.pdf
The other more elegant way (which would involve a lot of custom programming) is to work out when N2-N7 is being turned on, and insert your own high signals into B11,B12,B21,B22,B31,B32. This is probably a lot more effort than you’d expect. It’s been done before with other synths (see http://www.maxmidi.com/diy/sk1/article.html). Also, it probably won’t be possible with MIOS because you’d need a dedicated processor just to make sure B11,B12,B21,B22,B31,B32 are driven high within microseconds of N2-N7 changing, you can’t have MIOS interrupting this process.
So I’d go for plan A. Watch out for the very bizarre voltages! It looks like everything works on GND being “high” and -9V being “low”… this complicates everything, as I would suspect that IC1 also is running on a 9V difference between high and low… perhaps a 4066 won’t work then… and you’ll need some other solution to control the switches (i.e. relays). Someone with more experience with MIDIfication could help you there.