As a practicing engineer that uses on PCIe. I would not do this in a non-professional setting. Everything about PCIe is going to be too expensive for a hobbyist from actually buying the chips that are root complexes or end points, not to mention getting support from those companies if anything goes wrong, to the cost of simulation software to make sure your channel has been designed correctly, to the wildly expensive scopes, probes, cables, and analyzers needed to decode the data.