I bought a GoPro mount that I can get under the car, I'll take it for a few runs and see if I can see anything happening, but I don't think its movement in the parts.
I might try and get a GoPro headband as well so I can show you what is happening, as I'm pretty confident I know what is causing the harsh shift in a mechanical sense. I found somewhere really quite where I could just up shift and down shift without annoying anyone and I did that for a while. The car absolutely is not rev-matching on upshifts, but is revmatching on downshifts. Keeping in mind that it is a manual gearbox, it behaves like one when you shift. If I don't lift off then the RPM continues to climb making the shift harsher when the clutch engages. When I've been lifting off I've been doing the rev matching manually smoothing out the problem. It also explains why the issue is more pronounced at lower RPM, when the shift takes longer to happen.
So for everyone else, when you pull to up shift, does the RPM drop on the engine to match the engagement? Assuming it does, then I've got a direction to chase the issue!
Then the trick will be working out what sensor is meant to be feeding that information to the TCU that is getting missed. Or conversely, what command the TCU is sending back to the ECU that is getting missed.