There are 2 sets of u-joints in the steering column. One is inside of the rig and the other is outside. Which "intermediate " shaft did they swap out? I'm assuming it's the one that is outside... could be worth spending a little time under the dash to unbolt 2 bolts that secure the shaft inside the rig and just feeling what the interior U-joint is doing..

I have 0 faith in shop work or the troubleshooting they can do, be it at toyota or elsewhere, so what I would suggest.. if you don't find an issue with the interior u-joint on the shaft, is to disconnect both outter tie rods, get the front end in the air, and just manually turn each wheel left/right to see if you can feel any binding/resistance in either the upper or lower balljoint.

With the outer tie rods disconnected you can also give the steering rack a check by steering lock-to-lock left/right and see if you feel any sort of hard steering/binding. In the air with no tie rods connected you should be able to steer with your pinky with next to no resistance.