Have you looked into using a PRU for the real time data capture? There are two PRU units that run independently from the am335x processor. They are dedicated 200mz 32 bit microcontrollers with 8k program & 8k data. They also have the ability to interface with the BBB pins - even shift in up to 28 bits at a time. You can program in C or Assembly and get very tight timing loops to capture data. The PRU memory is accessible to the am335x, so you can build a buffer of real time data and collect it from Linux when it has time.
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