Y axis error turned out to be a drive ratio issue on the X after checking screw pitches and other areas, somewhere along the way one of the pulleys isnt the correct one for this model and it is no longer 2:1 between the nut and stepper.
Spindle vfd needed step pin drive with a generator adding to hal manually, rather than pwm. Its working now though and I understand hal a lot better for the extra bells and whistles getting added in future.
Two seperate gcode programs with touch offs between them to align, just a old piece of laqueered wood to test things on. And a satisfying blob of oil from the spindle being slightly overoiled while I order a replacement bjur metering valve for the head as I had to drill one out it was so blocked.

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