Ian & Jack, thnx for putting up all the details. I have gone through the info and updated the block diagram accordingly (I hope, I didn't miss anything):

1. corrected 1.8V --> 1.2V
2. corrected the SPI path PIC --> FPGA --> SPI Flash (saw it in Jacks design that no direct connection PIC --> SPI Flash is needed since it can be accessed through the FPGA - correct me if I am wrong)
3. added Ready/Done LED as suggested by Jack
4. added Trigger_Out signal to the 1st 2x10 header (good suggestion by bdsmith for daisychaining other equipment/devices)!
5. put a 16-Bit transceiver instead of the 8-Bit buffer(s) on the 1st header
I think the transceiver is really needed to make the device 5V tolerant on all 16 lines
6. added Ext_Clk_In signal to the 2nd header - very important hint by Jack!
7. added Trigger_In signal to 2nd header (suggestion) - so the device can be daisychained and triggered by other equipment/devices/special signal without sacrificing the number of input lines that can be captured (16/32).
i.e. When developing I like to set a port/line in my code to trigger the capture rather than to wait for some pattern on the lines that may never occur.
8. Added +3.3V to the second header becuase I think it will be the best option NOT to buffer the lines of the 2nd header! I suggest the second header to become the expansion and special features header - so it could be used for capturing up to 3.3V signals without an extension. Possible add-ons for the 2nd header are:
- 5V tolerant buffer board
- A/D board for DSO
- D/A board for signal generator
This will keep the cost for the project down and allow for follow up projects/add-ons.
9. added the external SRAM capture buffer from Jacks FPGA design. I doubt there will be place
for the (at least) 60-pin header it would require (if implemented as a 32-Bit interface like in Jacks design) not to speak of the routing issues on a small 2-layer PCB. I see it as an option for a follow-up design/redesign.
I am contemplating the option of spinning off a child project with the FT2232D. I would take the FPGA Cocoon board Jack is designing for Ian and design a "CPU" carrier board with the same foot-print as Ian but with the FT2232D instead of the PIC18F24J50. In the end we would have two boards that would run with identical FPGA configuration bitstream images and could use the same add-ons. Comments?
Uwe