8b10b clock recovery?

Yes, i suspected that jitter would be the main problem.

My initial though was to clock the scope with one of the signals in the differential pair. This, of course, means that jitter will not be measurable since the scope will always trigger on the rising (or falling) edge of the signal, effectively not displaying the jitter. Since i want to primarily use this setup to measure the signal quality after having passed the PCI Express signals through a passive extender board i am really only interested in the rise/fall times as well as the amplitude of the signals before and after the extender board.

My plan is to create my own PCI Express Load Board similar to the one once sold by intel. These boards simply connect the signals in the differential pair coming from the motherboard to a SMA connector that terminates with 50 ohm in the scope. This would enable me to use a low-cost 6 GHz bandwidth sampling/digitizing scope to monitor the signal degradation with and without the PCI express extender board. I would assume the jitter to be the same before and after the extender board since jitter would largely be a property of the transmitter, not the transmission line?

Also, would the recovered clock have less jitter than the signal it was embedded in? If not, i might as well just trigger on the measured signal itself instead of recovering the clock.

Could you recommend an external clock recovery circuit?