It looks like an ATMega32U2 is the best option for the controller, as it can do full speed USB. Along with that, it appears like a good choice for the framework for this will be the LUFA library. I have only spent a few minutes looking into it, but it appears that there is good demo code available for a mass storage device. Plugging in the crypto and the SPI interface to the SD cards looks reasonable doable, at least from here.