I have used softcores for ordinary PCI supplied by FPGA manufacturers and they can be very restrictive in what they allow in terms of the types of target you can have and how the the thing is set up, the Xilinx one for example, simply will not work except for one very specific device.Xilinx supply a UCI file but that means you cannot ever change the pinout without breaking the timing. I doubt you would get PCIe to be any more flexable.Opencores PCI cores are probably a better starting point but I still wouldn't recommend it unless you really know what you are doing with HDLs and FPGAs.
You are talking top end FPGAs which are PCI complient let alone PCIe, big bucks which would not be compatable for a small project like this.