You really want some hardware to preprocess the
signals somewhat.
Has anyone considered using a DSP?
Also keep in mind that those ARM SOCs as used on the
RPi
or Beaglebone Black have some rather sophisticated DMA
capable SPI, PWM, ... peripherals.
It's more expensive that something like a Beagleboard, but TI has a line of
ARM processor + TMS320 DSP chips (like the TMS320C66x series) that seem
like a perfect fit for this application. Use the DSP portion to
capture/pre-process the bitstream and the ARM to interpret, structure and
store it.
Just a thought.
KJ