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Exactly, the PCIe reference clock is "only" 100MHz.

USB 2.0 runs at 480MHz and motherboards have used 0.1" headers for them since the beginning.

While the ref clock is only 100MHz the data rate of PCI Express is much higher, it's a serial bus pushing multiple gigabits a second https://electronics.stackexchange.com/a/259002

Yes, the theoretical maximum (nyquist freq) of PCIe 4 is 8ghz

The Pi4 isn't PCIe Gen 4, though. It's only PCIe Gen 2. Max speed of PCIe Gen 2 is 5GT/s, which equates to the same speed as standard USB3.0/USB3.1 Gen1/whatever its called nowadays.

Nyqist frequency of 2Ghz for PCIe 2 (slightly less in practice due to line code) is still nothing to sneeze at.

2.5 GHz, actually. Obviously there's limitations and you have to be careful, but it's not too crazy to think you could use a piece of USB3 cabling to do this. Requires some pretty precise soldering skills though.

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