Well I started this morning by removing driver side battery to look for missing wire. No missing wire, but while I had the battery out I decided to do a thorough cleaning of wire ends which attach to the post at the negative side. I believe this is where one of the wires got dropped in the 2012 post on the Cummins site. Anyway I finished cleaning connections, reinstalled battery, and reconnected posts. Shazam, no more flashing engine light or clicking, truck fired right up.
Here's what I believed happened. When I was removing the old batteries I used a baking soda/water mixture to clean off some corrosion from the negative side wires and post. Because the bolt was loosened to allow the cable to be removed from the post, some of this mixture got down between the wire ends and hardened. This was preventing good contact when I reattached the cable with the new battery.
I so much appreciate all of the help, especially all of the good detective work to find similar issues that might shed some light on my problem. When you have no real skill at working on vehicles it's just really easy to convince yourself that your not capable of doing even the simplest repair. I can't tell you how greatful I am to have people willing to offer their assistance.