Hey guys, it sounds like you are trying to do exactly what we did last year with Chicken AID. The only difference is we used a USB thumb or an SD card. We used a development board that we created to prototype Chicken AID. The Board uses SPI to communicate to the SD and USB host. We use USART to communicate to the R/C the board has a built in RS232 converter.
Here is the link
http://www.crosstheroadelectronics.com/uPICFAT.htm
The development system is around $150. But it is a complete, out of the box solution. It includes the board, the plug in with examples, it also comes with a power supply, LCD and serial cable.
Mike Copioli
CTRE