I've had a bit more of a look around and it looks like the cup end pogo pins can be used to test connectors?
Maybe I'm wrong, but it seems like it would be as easy (or as hard) to test the connector directly with a pogo pin as it would to test a pad on the PCB...
I will have to manage misalignment of the connector as soldered onto the board.
I've done this for JST ZH (1.5mm pitch) headers using standard 1mm dia cup point pogo pins, aside from the spacing being very tight it works fine. As you go down in pitch the size of the cup becomes more critical, since it needs to be big enough to reliably accept the pin on the DUT, but small enough to not cause a clearance issue between pins. The alignment of the board to the fixture also becomes more critical of course, so you might need to take extra measures there. Using pins in the fixture that align to tooling holes in the PCB would be a good idea rather than relying on the board outline to locate the PCB.
PicoClasp are rated for only 30 mating cycles, so I’d be leery of using them for your test jig since you’d have to replace them frequently, even if they exceed their rated mating cycles in practice. And alignment might be an issue too.
Since the limiting factor on mating cycles is usually contact resistance exceeding a fairly low threshold, you can get quite a lot of tests out of a set of connectors if the current requirements are low enough. I don't think there's a likely mechanism for a worn out plug to damage a brand new header after one short use, aside from overloading a high resistance contact? And of course physical damage if the plug is REALLY beat up. It's also possible to incorporate a contact resistance test into the fixture/test procedure to catch a failing harness before it causes a problem. The downside is it requires a redundant connection for each monitored net, which could be the same net on a different connector/pin, or a test point on the board -- or some support from the DUT, maybe. But it might be a good option if the connectors are all low current signals plus power/ground.
I've also thought of taking a connector plug and shaving it down a bit so that the insertion force is much lower, then attaching this to a jig somehow.
I've done this as well, although just for manual plug-in tests. At least with ZH connectors IME, the first thing point of failure on small connectors that get cycled a lot is the contacts popping out, since the wires inevitably get tugged on while unmating the connector because there's so little connector to hold on to -- which would also make to hard to mount the connector in a fixture, especially in a way that can withstand the removal force. The other problem with using those connectors in a fixture will be aligning them to the headers. Remember that there is a certain amount of tolerance for the position of the connector on the board, so just mounting the connectors very precisely and very rigidly in the fixture won't work. The fixture connectors need to be able to 'float' and self-align to the header somehow. Maybe you can modify them with a lead-in chamfer on the front or something, but they'll still be somewhat consumable, and will be harder to replace if they need extensive modification.