When I reassembled everything, I noticed that the X axis ballscrew seemed to be bent - the ballscrew nut mount was flexing noticeably as the screw turned.


I took it out again and got it centred up in the lathe and while it had some runout, I didn't think it was that bad (something like 1mm runout over ~400mm). Nevertheless, it seemed to be causing a problem, so I decided to try and straighten it.

I set the lathe leadscrew to the same pitch as the ballscrew so I could run the DTI down the ballscrew thread and plotted the total runout along the length.







Sure enough it had a couple of kinks in it (a small one at about 40mm and a bigger one at 100 mm - both in the same plane):






I managed to get them out by leaning on the end of the ballscrew with it held in the lathe chuck next to the bent bit, and got it running reasonably true. When I put everything back together, the ***** thing was still running out.


To cut a long story short, I eventually traced the problem to the way that the thrust bearing was mounted on the ballscrew.

The bearing arrangement is a standard FK type flanged block with a couple of angular contact bearings and a short spacer either side. The end of the ballscrew is machined down (by the manufacturer) to take this assembly and it all gets clamped into place by a locking nut. What was happening was that the spacer was a bit of a sloppy fit, and rather than bearing evenly on the (small) machined shoulder, it was bearing on a single point at the end of the ballscrew 'thread' - Tightening the nut was bending the ballscrew.

Once I'd figured this out, it was easy to make a new spacer that was a tight fit on the end of the ballscrew (loctited in place for good measure) so that the load would be transferred evenly to the ballscrew.





Runout with the original spacer (it ran true when the clamping nut was slack).




Runout with the new spacer:




With everything squared up, and the spindle trammed, I was still measuring a bow in the plate used for the Y axis carriage: +/- 0.07mm in the worst points.




The X axis had been set up straight to the glass plate and I went around in circles for a while trying to decide whether it was the glass plate or the Y carriage that was out, and whether the Y guide rail mounting was pulling the carriage out of true, but removing the Y axis carriage completely and checking it with a straight edge confirmed that it was much less straight than my glass plate.
I didn't want to pull my nice new table out of true, so I would have to trust the machine to skim the Y carriage flat (I know NOTHING about CAM or CNC programming, so feeds & speeds were, at best, educated guesses):

Some video snippets of the first, tentative cuts...

Taking the first 0.1mm off the Y carriage plate:




Another 0.1mm fully cleaned it up:




Flushed with success, I got it to drill and chamfer the matrix of fixturing holes as well:







I had to tap them all by hand though ...