Yes, I use BBBs as standalone system. But I don't connect a keyboard, mouse 
or screen. Instead I connect LAN and use the PC to control the BBB.

On LINUX it's simple to remote control other systems over LAN. It doesn't 
matter which version is installed on PC or BBB. (But when both versions are 
based on the same distribution, like Ubuntu is based on Debian, you need 
not understand different file systems.)

Don't use cross-compiling at the beginning. You'll face a bunch of 
additional pitfalls and it's complicated to help you in case of any 
trouble. Just store, compile and test your software on the BBB (SD card).

Your project sounds interesting. Another user of libpruio made a low cost 
EKG system.

I learned

   - type: low speed controller with complex signal processing.
   - input: analog from Brain Computer Interface (number of channels?). 
   What about the former mentioned 'lengthy calculations'?
   - output: 1 PWM signal to a H-bridge.

The BBB can sample up to 7 channels of ADC data (12 bit, 0V to 1V8). 
Further channels need additional hardware.

The BBB has up to 5 PWM output pins (0.5 Hz to 50 MHz).

The project seems to be doable.

BR

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