fpga schematics
0. place FPGA near to the edge of the board.
1. print out FPGA pin map.
2. print out PCI pin list and draft.
3. assign the fpga pin to PCI pin (short distance is number 1 rule). use dedicated bank for PCI. well use separate vcco for the bank if possbile.
4. if you need host power for add-in card(FPGA board), add de-caps on power pins
5. if you don't need host power, cut off power lines (to protect FPGA from accident)
6. pull-up several control signal pins(refer to pci spec) - optional.
if the distance from the edge of the board is short enough, you don't need the trace length equalization.
* I think that general connector and custom riser card pair is easier to handle.
you will not be limited to make the board 1.6mm thick.
* on Avnet board, they use buffer ICs for signal lines, but I don't think they are needed.