Yeah, sorry for being confusing. I had two separate issues that happened around the same time, which made me think they were the same cause.
First, I lost a stock cooling fan several months ago. The motor ceased and unbeknownst to me, burned up some of the harness going to the BEC, and part of the BEC itself. I put in a new fan, but it was still intermittently failing due to the bad wiring. Once I found that bad wiring, it took me two freaking months to get a new BEC and harness from Ford, but that fixed that issue.
But the gremlin was still getting stabbed, so that caused me to trace all of the wiring in the cabin. That's when I found the pinched door sill wire, which was my fault... wires moved around during installation.