Martin C – ha ha, its true. I spend my day being pragmatic and cant stand others who delve in to things that really don't matter. At weekends I like to chase perfection for fun even when its stupid, which is most of the time 
Nigel B – you are absolutely right. NRR or non repetitive runout is often caused by rolling element size differences or shape errors. Its non repetitive because their own rotational speed relative to the raceway surfaces, and their speed around the bearing is not synchronised with the ring rotations. so they can produce almost random-like motion in the rotating shafts. NRR used to be a big challenge on computer hard-drive spindle brgs where precision was all, but I have never heard of it being and issue in big brgs before. Good to hear about your case.
I have just rechecked my spindle face axial runout with the 'Hoppers Elephants foot' and it has really cleaned things up. Here's the set up:-

And here's the results:-

The spindle was turned by hand and the DI was pulled back to go over the bolt holes. I was careful not to touch the slides, (which I forgot to lock down anyway!)
There is an obvious underlying runout but there is also clearly a non-repeating element to the figures of around half the magnitude of the fundamental. As was suggested by Michael G, with a very fine and slow grind, one could remove another micron or two from the repetitive runout but there is no simple way of removing the non-repititve part without improving almost every other part of the machine. Its difficult to say precisely what's causing the NRR but the main contributors have to be the drive train and bearings
When I got the machine the belts (6 ribbed poly-vee) had a pronounced sets moulded in and these caused an audible bump every time they hit one of the pulleys. So I sliced the belts into two 3-ribbed pieces and staggered the moulding inconsistencies. This really reduced the noise and although I didnt think of it at the time must have helped the true running of the spindle. Perhaps there are some better belts available which wont cost an arm and a leg. Of course runouts in the pulleys themselves will cause load variation too.
As for the bearings, these are just standard precision eastern European taper roller type. There is no point in using a better quality product as I already know the housings are quite poorly machined. It makes no sense to put a good bearing in a rubbish housing because the geometric errors just get carried through to the raceways. I have actually wondered about replacing the TRs will ball bearings as a simple "upgrade". I know some people will frown at this say that its going the wrong way, but the advantage here would be that because the balls are more compliant they will absorb some of the geometric irregularities instead of passing them straight in to the spindle.
I'm certainly not going to be short of things to do when retirement arrives, that's for sure ! But for now I think I've just about done as much as I can with the spindle on this bag of old nails, short of speeding real money.
Gerry