I removed the print head from the printer, measured the distances as per the vertex instructions, guess what, perfect. When re-assembled I noticed that when inserting the second rod on the x & y axis (rod into the frame bearing that is) the rod naturally wanted to be either further out or further in.
With that, I set about sliding that rod in and out and gently moving the sliding block on the end of the print head rods until it was just perfect for both axis.
I used the alignment tools to hold the rods parallel while tightening the belts and pulleys (belt gears on the shafts with grub screws) a little oil and that’s that.