vfillion 49 digital inputs (different knobs and pots)
these sound like analog inputs? Unless they are rotary encoders?
vfillion 16 switches (8 killswitches, 8 regular on/off switches)
Is the killswitch a switch in series with an audio signal to "kill it" (e.g.: short it to ground)? In that case, it could act directly on the analog signal after it has left Bela. If the functionality is anything else than that then it probably needs to go into one of the digital inputs.
vfillion 8 audio inputs to outputs (1/8 or 1/4 jacks, to receive Bela signal and patch it to 8 differents mini-speakers outputing into wooden tubes)
What is an "input to output"? Is it just an audio input that you will then route in software through some processing to an audio output?
It looks like in total you need 8 audio inputs and ten audio outputs, alongside 51 analog inputs (2 for the 3-way switches, the others for the knobs and pots) (fewer if you are using encoders) and 8 or 16 digital inputs (more if you are using encoders). Assuming these numbers are right, you would need a BBB (CPU and 16 digital inputs) + CTAG Beast (8 audio in, 16 audio outs) + Bela cape (2 audio in, 2 audio out, 8 analog in, 8 analog outs) + Bela multiplexer (multiplexes the 8 analog in to 64). That's a 4-board stack but it works. It has several unused channels though (2 audio in, 2 10 audio out, 8 analog out). If you could sacrifice two audio outputs then a smaller and cheaper setup (BelaMini + BelaMini Multichannel Expander) would give you 16 digital in, 8 audio in, 8 audio out and 8 analog inputs. You'd need external circuitry for the multiplexer, but that's pretty straightforward to design if you have any experience with PCB design and you may integrate it in the PCB I'd assume you'd be spinning anyhow to hold all of the controls.