X-axies is not problem i think, and for your non existing Y-axies you loosen the turret screws a bit so you can adjust the turrets rotational position by gently hitting it with a mallet until its centered. The main disadvantage of this technique is, you cant adjust its y-axies for every single tool, just all toolstations at once. You can also try to shim between the Tool and the Turret. But be carefull you could also deflect yours tools axies depending on where you shim, what kind of turret you have and which Mounting-system your turret has.
