Totally agree with you on wear as the machine is new. Not completely sure about the rebuild, things could have gone awry there, due to an error or some alignment of all the gear shafts, or there's still some hidden damage present. It's still detective work at this point... Best we can do is suggest some diagnostic tests that might give experienced people like you a clue.
Pardon my ignorant questions, but if the lead screw pin was broken, or the lead screw can move along its axis, couldn't that give different cuts in the work piece, or yield inconsistencies? I mean, something's wrong, so we can't assume everything is working perfectly.