What you wrote is the same that I found. Allignment is very critical. My leadscrew bearings are flexible in a spherical housing and I can move them up down and left right. So I move the gantry to one side with loose bearings, then tighten them, move to the other side and tighten them. I repeat this process a few times. On my next CNC I would mount the lead nuts floating to avoid that issue. But now I make more money and I could just buy a ball screw. However this method could be useful for other stuff like router lifts or tablesaw jigs.