I bumped up the acceleration to 1200mm/s/s and tweaked the gantry which was out by a few tenths of a mm with the autosquare. I will be moving house in a few months so I will check then to see if there is any wear from any slight binding but it runs fine.
I dropped the backlash comp on the X to 0.1mm, and will see if I can drop it some more with a couple more tests tomorrow, but the holes are spot on now.

Thanks again for your input, much appreciated.