Thrust bearing / throw out bearing is the bearing mounted on your clutch fork which is pushing on the pressure plate as it rotates and you pushing the pedal; hence thrust bearing.
Well There are some judder, but I take that it should be there as its a Alcon 6 paddle...íts done 10-12000km so I hope that there are some miles yet before it's worn ..??
That depends on how good flywheel condition was prior to install of the new clutch.
I do a lot of work on T5 / TKO transmissions and the problem you are having tells me its most likely the clutch not disengaging properly. If it was the gearbox then it would make
grinding noises as the selector trying to engage gear but is not able to syncro (worn syncros).
My GFs BMW just experienced this juddering and the thrust bearing / throw out bearing was totally worn out. This made the pedal judder.
I ran the Alcon 6 paddle for 3 years before now making a total driveline change; it should not judder your clutch pedal. Actually the Alcon should feel just like a normal Toyota clutch.