I'm trying to go in chapter order and Chapter 3 works with two minor problems.
3.6 Mark camera to Nozzle 1. The manual asks that we "setup a new part at the adjustment position". At this point in the bring-up I don't have any parts or boards yet defined. I don't know how to perform this step. What I did instead was to use the "visual origin" as the reference. I used a small head and moved XYZ until the head was exactly over the mark. Noted the XY values and moved the camera to the mark. The difference in XY values gives the needed offsets.
3.11 Mark Camera Properties Again not a big deal but I tried to set the values and could not. Of course not, the values are part of the PCB project now. We can't change the software but maybe move 3.11 into the chapters on adding a PCB???