Well, the second dealership called me this afternoon. They located a "master wire harness" behind the dash which had been "crushed" during the build process behind a large metal reinforcment tube. The tech tells me that it was at a 90 degree angle, and it's a wonder the truck ran in the first place! Needless to say, all has been repaired/replaced, with big apologies all around. They threw in the installation of my TPM sensors, a bed cover and free oil changes for the trouble.
Drove it back just now and all minutia of problems have disappeared! Amazing huh?
But now to the pissy news (for which I will start a new thread)...
"We received a service bulletin last week... all 2008's must run
Premium Fuel!" 
WTF!