A couple of thoughts which may or may not be worthwhile –
(1) I don't think the test described on page 38 actually checks that the spindle is perpendicular to the table, only that the table is flat – the spindle could be cocked over at an angle and the clock reading would still not waver as the table was run to and fro. To check for perpendicularity you need to mount the clock on an arm at a fixed radius, pointing downwards, and swing it round to different positions.
(2) Obviously the LH x-axis handwheel shouldn't be rubbing against the endplate. However, "…the right hand side of the x-axis leadscrew had the same dual thrust bearing arrangement as the AMA25LV…" (page 39), apparently to cope with thrust in both directions, so it isn't clear to me why the LH end would need a thrust bearing as well. After all, two thrust bearings at one end work for the y-axis. Maybe this is why the makers omitted the extra bearing on the AMAT25LV.