Nice project. I wrote a simple high-speed logic capture firmware for the AVR atmega8 a few years ago, and have been thinking of doing something better with the STM32 ever since. I have a fx2lp-based logic capture device that works well up to 12Msps, and find most of the time 1 or 2 of the 8 channels is all I use. With a 74HC595, and some minor additions to the buck50 firmware, you could support single-channel 48Msps logic capture. The STM32 needs to output the 48MHz clock to SRCLK, and a 6Mhz clock (or whatever speed you are reading the 8-bits of data) to RCLK. The input would be hooked up to SER.
Using the same concept with 2 shift registers, 2 channels at 24Msps should be possible.