I think that for a first approach you should forget about PCI: in this case you need to make working not only the pci IP, but also the driver. My suggestion is a medium size (100k-300k gates) FPGA, which can be found relativately easy and cheap:
A C E X or C Y C L O N E from @|ter@, or
S P A R T A N 2 E from X I L I | N X
- Don`t forget to get out all the pins
- Don`t forget clocking: try to use FPGA with PLL on board and have the possibility to introduce the external oscillator, via outside clock with a BNC or with something like a clock generator in the board if you don`t have PLL inside the FPGA. (Cypress for example, have some lots of them)
- Possibility to load the FPGA directly from external cable or loading an exteral EEPROM. You can also have the possibility to load from a uController.
- A fast memory on board could be also nice, as well as a flash.
- LEDS, jumpers.
- buttons for reset...
- An ethernet or serial port.
As you see, the board can be as easy or difficult as you want.
Regards