FPGA (with
maybe some small amount of external SRAM). This would also have 
 the
  advantage that the whole hardware configuration
could be changed by
 downloading it from the host if needed for more exotic floppy formats... 
 Hmm...
Good idea.
 FDD --> Xilinx FPGA --> FDC
 I might have to try that. After I build my EPROM programmer. 
 
Try using CPLD as a FDC since they have the advantage of onboard
programmability and power up configured.