Thank you for your response. The CONF_DONE error occurred because I moved the pin over to add the PCI Express to the JTAG chain. This did not need to be done. Now I have the Arria II GX (125 variety) dev board programmed correctly.
Does anyone know of a good way to confirm that everything is working with the PCI Express design? My goal is to bench mark latencies from reading data off of the board to user space memory and back to the board. I can't seem to see the PCI express design working on the board yet using signal tap or be able to read and write registers correctly. Anyone have any ideas of how to make sure the design is working or do the memory benchmarking? I tried using the program and reference design combination mentioned in the above post but all the data transfers fail but I can read all the system registers.