It is (of course) up to you, but I would suggest combining some of the functionality of the 3 control boards you described into a single RPi Cape. If you include an Atmega/Attiny on the sensor array board, to do the 16 channel counting, and wire a UART/i2c/SPI interface to an RPi Cape, that also had Stepper motor drivers onboard (ex Pololu A4988 modules) you could significantly decrease the cost of the control hardware, not to mention avoiding running shielded USB cabling all over.
Just my 2 cents!
Thanks
P.S. I can't wait to build my own!