Hi xjdubber,
I will apologise now for what I am about to say.
Don't apologise
Agree with you on every point, except for the first (and some others:)). Im sorry but I've never seen an over size cutter yet? as for the rest, I agree but then those points should already have been taken care of before setting accuracy. As for the acuracy on the ballscrews that really depends on how new they are. Also squaring the spindle is not going to change the lenght of a cut. On your point #4 what do you mean 1" even normal size digital calipers go up to 6", You think i would measure error out of a 1" cut?
I have setup 6'x20' routers, that run anything up to alluminum that hold tolerance of .005 over 10 feet, so far the way i do things has been working for me