I think you have already narrowed the search to the likely culprits;belts would be more likely than couplings but its worth checking both.Depending on the feed speeds you are using and the depth of cut it could be the gantry or the spindle mounts flexing.Have you tried locating a dial indicator against the collet nut and pushing with your hand to see how easy it is to deflect the needle?Try it both in X and Y to see if there is a difference in the force needed to achieve the same deflection.