I think the best is to actually buy an FPGA and learn by doing it. I spend a couple of days to run some calculations and these products seems to be the best regarding Mh/s and low power consumption:
- X6500 FPGA Miner
- ModMiner Quad
- BitForce SHA256 Single
I know micro-controllers from industry automation (you may have heard of Advantech from Taiwan) and as long as these Bitcoin boards contain a Watchdog they should run super stable and be easy to use. Guess today only Spartan 6 chips are useful, so no matter which board you buy the procedure to get it running should be similar.