Thanks, Nick - you got there first! I did some quick back of envelope trigonometry earlier and reckoned that any misalignment that gave that linear error would be so great that even with my eyesight I would see it. My ballscrews are about 1700mm which I reckon would put one end about 76mm out of line.

I'm also using Hiwin rails as well as ballscrews; you either use accurately machined mounting surfaces (just not possible without access to some pretty big kit) or you build in adjustment. I was surprised just how unforgiving of misalignment the Hiwin rails are. I have adjustments available at all key points and, not surprisingly, used the method described by Boyan (although I suspect that it has been described many times before). However, I have been using a vernier caliper (not digital, unfortunately) and although still in good nick and a reasonable brand, it's not really to be relied on at this level of resolution. I've no idea what the realistic accuracy of a vernier caliper is as I've only found mention of reading resolution which is not quite the same thing. Maybe the Easter bunny will bring me a decent digital caliper, by which time my garage temperature might even be approaching the nominal 20degC required