Yours is a decade older than mine, but my diagnostic work involved pulling the plugs off the controller box (an HWH box located on the roof of one of the bays) to check for voltages, found nothing out of order, but when I plugged them back in the thing worked fine.
Dirty connections seemed to be the issue. Not very satisfying when you can't point to a specific failed part, but that is the way it goes. Worked fine for 3 years.
2006 Patriot Thunder C13 Allison 4000
2010 Ford Flex Ecoboost AWD