I was talking about the Arduino Due, which has a Cortex M3 processor and uses 3.3v logic, NOT the Arduino Duemilanove that you are thinking about.
But if you are willing to dive into FPGA programming, I admire your ambition. I don't think my old brain is still functional enough to take on that level of education. Best of luck with your project!
John Toscano, W0JT