Well, the issue seems to be resolved, but I'm not sure why.

I took the alternator to a reputable auto electric shop (what a cool place!) and the owner verified the alt was good. I watched him get 14.1 D+, and 14.0 on B+. He was extremely confident there is nothing wrong with the alt, so I re-installed the alternator and took some measurements:

Engine off:
Battery: 12.58v
Resistance: Alt case to battery neg: 0.2 ohms

Engine running idle, no DRL or other load
Battery: 13.80v
Battery+ to engine bay body panel: 13.80v
Battery+ to thermostat housing: 13.80v
Alt B+ to engine block or alt case: 13.84v
Alt B+ to battery+: .022v
Alt D+ to alt case: 14.10v

So I'm getting a solid 13.8v at the alternator. Note that last year I ran a #4 B+ cable directly to the battery (disconnecting the alt-to-starter cable), and a new #6 alternator ground to the engine block cable. I think my original issue is solved (not sure what changed) and I can call the alt to battery connection 'good' for now.

On to the next fix it item... Battery to fuse panel - should be fun.

Thanks again for all the discussion and help. Much appreciated!