Well I finally got my Exped repaired.
It took a 24hr road trip (6hr there, work time then 6hrs back) to get everything fixed...but it was free so we couldn't complain. Joe Watt Auto (where the SO bought our rigs) did all the work and bought me a hotel room so I could sleep while they worked.

Turns out on the pass side, the spring that the truck uses for the variable cam timing failed so stuff was flopping around and causing the motor to be out of time w/itself (periodically) which was causing all the clunking/clanking/rough idle/CEL/flashing CEL/etc.

They went ahead and replaced timing chains while they were in there too.

Maybe this will help someone else fix their issues.