Stratix4GX PCIe development board to used as root port

You can’t not use the main processor on the mainboard. You can’t re-route the the root port activity to a processor behind a PCIe link. All PCIe activity is initiated by the operating system on the CPU behind the root complex, and that’s only the main CPU on the base board.

If you really want/need to have a custom processor act as the PCIe root device, you have to build your own motherboard. Especially, if you want to use a standard COTS chipset you have to mimic the matching CPU local bus (or HyperTransport, etc.), but then you don’t need the PCIe root port in the FPGA in the first place.

PCIe is strictly top–down. On top there is the root port, below are end points and switches. No way you can “reverse polarity” on a link and let an end point act as a super-root complex, disabling the main CPU.