I spent a while last night taking more measurements of the thrust bearings and mounts. The two thrust bearings and mounts have very different behavior.
The lead screws are constrained only in the coupler and thrust bearing. I've got a sliding platform under the X carriage ends that allows the lead screw to move freely in X and Y.
The bearing, coupler and mount that I have on the left side seem to be stable, with no measurable movement in X, Y, or Z. The left lead screw is not parallel to the smooth rod, but there's no X,Y motion at the end of the lead screw, just rotation.
The right side is a different matter. I also collected a few additional measurements on the right side. With the dial indicator on the outside bottom of the flexible coupler, I saw variance from -0.02mm to +0.05mm separated by half a rotation (which didn't seem too troublesome). At the top of the flexible coupling, I saw variance of -0.01mm to +0.05mm separated by half a rotation. That matched the bottom.
The thrust bearing was an entirely different story. Measuring displacement in the X,Y plane, I saw variance of -0.15mm to -0.01mm, which didn't seem good, compared to the left side. Then I measured displacement in the Z direction from the top of the thrust bearing and saw variance of 0.00mm to 0.05mm.
I can't work out the geometry, but I suspect that the lead screw is in a canted hole and some of the eccentricity is showing up as Z movement.
I've ordered some couplers to see how that affects it.