Not quite sure why the bearing retaining washer would have shims. The nut tightens the inner race (s) [I think there are two bearings back to back on the thrust side] to a shoulder on the ball screw. The retaining washer tightens the outer races to the housing. All of that should be solid so if there are shims in there that might be the problem. Neither the washer nor the nut put any preload on the bearing.
You said you have adjusted out all but .001 of slope; What were you adjusting?
You can buy a spanner wrench to the nut or just make one.