Well seem to have fixed it all.
Printed a plastic pencil holder to run up and down the side of the table to check the alignment. Less than one pencil lid in deviation!
I loosened the gantry head on one side and really squeezed it up against the table. All sorts of little things go into this business obviously.
Here is the .stl of the pencil holder if you are interested.
Pencil holder for axis checking.zip (160.7 KB)
Rob