So I was able to identify the source of the noise as well as homing in on the problem. Video here. The sound was coming from the lead screw being twisted by the weight of the gantry. The lead screw can spin (not freely, but it has some give). I am now at a crossroads with the troubleshooting, if it's the controller side or inherent to the servo.
A) The servo will attempt to move but seems to be skipping a phase or something.
B) I can still feel the magnetic ticks on the lead screw, so it seems to have a good mechanical connection, (the problem is likely electrical.)
C) An awful grinding noise is made as the stepper attempts to move. It is able to be moved by hand with relatively little force (something I've never seen a stepper do.)