Jeff,
Brilliant, detailled honest review. You have done well to maintain the matter-of-fact tone of your posts as you work through the challenges of a new printer.
It seems to me however that you are experiencing many of the types of issues that those of us who bought a printer at the cheaper (much, much cheaper) end of the market have to deal with.
I seriously considered a MakerBot before ultimately buying a 3DStuffmaker and did initially think that perhaps I had made a poor choice when it turned out that you really need to dedicate some time to learning the quirks and odd behaviors of the lower end printers (what a n00b I was back then), but it turns out that the 5th Gen Ferrari is slower and just as temperamental as any other printer.

I struggle to see how MakerBot can justify classing this printer as a generational change when very little seems to have changed, certainly very little has improved.
Many aspects are different but hardly improved. Smart nozzle? That's more effort to clear a simple nozzle blockage than I have ever dealt with.
At this rate of "improvement" the Gen 6 wiii take 4 hours to prepare to print and 4 days to print a rook.