First up, I felt that the acceleration I set before was probably not the maximum possible. So now we have 6000mm/min and a full 1000mm/s2 in acceleration. That is pretty stiff.
About an hour of work later, and both the vice and the fourth axis are mounted and squared.
One thing is not great, though. It seems the the Y axis bearing has somehow set and now has a full 0.1mm backlash. I guess that I will have to take it apart and fix that. Fortunately I realize I can do that without affecting the rest of the machine. But I still need to remove and reattach the ball screw. So not very happy about that.
So for now it has an official tolerance of about 0.1mm all included. So I felt I neede to actually do something with it.
So if you can see it, the Delrin piece has a big hole in it. It seems Fusion starts each program with a g53 move to z0. Now I had configured 0 to be at the bottom of the range. BAD IDEA. Had this been anything other than plastic, I would have been one endmill poorer right now.
But I did manage to fix one more thing as well. Now the Linux CNC accepts a tool in the G-code. So no more custom processors.