Well it wasn't the ball screw. And towards the end of the four hour procedure of taking the x and z axis sufficiently apart to disect the ball nut, sort the balls, and reinstall them, methodically sorting and spacing the 15 of 212 that are smaller, and then putting it all back together, I realized there was a much easier test. I should have simply decoupled the motor from the screw, and used a tick mark in the outboard motor shaft to see if it was still losing steps even without the motor connected to axis. This would have revealed to me ,as it did,that the problem was not the ball screw, or anything in the axis, but electronics or settings. So, wasted time, but knowledge gained.
And the answer is : Motor Tuning, Step and Dir Pulses, If they're at 0 set them to 5. Thanks Chip! It also smoothed things out a bit to enable "Sherline 1/2 pulse mode" in ports and pins.
I still have annoying resonance issues at mid speed, I guess the notorious "midband resonance." I'm using Keling drivers and steppers and BOB, the 640 OZ/inch motors and KL-6050 driver on x and y, with the KL-8078 on Z.
It's not really a problem on Z, where it midband, expresses itself dramatically. With its 2 mm lead, it runs very smoothly from 1-38 IPM or so, and then stalls completely up to about 50, then smooth at higher speeds, but I"d not want to go faster than 50 anyway on Z, and a reliable 35 IPM is actually fine speed, even for the joint cutting work with router horizontal I'll be doing.
On X, with its 20 mm lead, I get best results microstepping to 1/16 th, and then it runs smoothly up to about 60 inches minute, and smoothly again at about 90, and can go to 300 IPM fine, even at 1/16th mictrostep.
Y, with a .5 lead two start "no name" screw with a little roughness in the screw in a couple spots is good to about 18 IPM, and then bad to about 35 IPM, really atrocious in the middle of that range. Then it runs better, smoothing out beautifully at about 50, and can go to at least 120 IPM, far faster than I'd expect to use it. A little more experimenting with settings, trying switching the drivers on Y and Z, to se if that helps quiet the Y at its resonant speeds. This is amzing stuff-- not exactly intuitive, is it?