Hi Neil.
Martin and John have had the same issue as i have had but mine was after a rebuild because i fitted a belt drive kit
This required the two halves to be split to remove the gears and to fit the sensor for my digital tacho .
I used an angle plate to test the alignment of the column by clocking it vertically then trammed as usuall .
I ended up leaving the head to dovetail screws loose enought so i could tap it with a plastic hammer to adjust then remove and tighten – thankfully nothing moved when i lifted the head off the column to tighten the bolts !
If you don’t own a reasonably large angle plate clamp a parrallel to the one you have to extend its range or if you don’t own an angle plate clamp the largest known good square to the table and clock the blade vertically .
Yes i know it is not as good as a precision cylindrical square but make do !
I suppose if i went insane enough to worry about it i could set the column up on my large mill and machine a locating step into the dovetail bracket and then do the same to the head to locate it parrallel to the column but thats another job to think about !
If your readings are in error in the Y axis try removing the column to base bracket and check for burrs or any debris between the mating surfaces – wouldn’t be the first time gunk has been found under there !
Ian