Could you explain why you chose to use external ADCs, and not use the axoloti ADCs directly?
I would consider using for example the axoloti DAC pins as CV outputs, and the remaining 13 analog in pins as CV ins and potentiometers. That leaves still some digital IO for gate/clock functions.
Another suggestion: you use a precise -10V reference for the level shifting, but the Vref to the ADCs is provided by the 7805 which has much larger tolerance. If you derive the shifting voltage also from the 7805, it would give a better defined zero level of the analog ins (may need one additional opamp to do this).