Is the machine square if you take the middle assembly off, meaning the rollerf’s connected with the rails? If it is square with out the center on, I am with shaneEEEE take the center assembly apart, but leave it on the rails. As you assemble it, one piece at a time verify it is square at each step. That is how I build them now, I will update the instructions when the new center is released.
y axis, if it is making noise take the belt off and power up the y steppers and hold the pulleys in your hand are they both turning with about the same force? We used to get a lot of wiring issues before the wiring harness, this was a common problem. If that isn’t it sand down your rails a bit.