Looks very interesting. Thanks for putting that online. I just looked at the CPLD code and it seems pretty straighforward. It seems from your comments that you worked more on the FX2 than the CPLD. Was the CPLD tested in hardware?
I also digged into the FX2 code. I'm trying the code as-is, although I'll have to change the PortC to something else (I'm using the 56 pins version of the chip) and I'll want to simulate an FTDI chip eventually.