Good find & feedback on the wiring short circuit.
Fuse 19 blowing would have been a good clue on the stall, as its for the PCM power diode, Ignition & PATS.
Is it running ok now????
If you documented what you found with plenty of photos & the shop is professional, they may offer at least their cost of the wiring harness, worth a try.
Let us know how it goes.

 

Pictures, a factually written emotionless statement from another mechanic, the invoice from your tow, and a firm but pleasant face to face handshake with the shops owner will usually persuade them to take care of it for you. If you keep calm and talk to them civilly they usually don't have issues making right when caught. With all this "evidence" in front of them any mention of a lawyer will make then hesitant and eager to settle out of small claims court, especially for an invoice so small.

Realistically any lawyer wouldn't bother with something like this and its not worth the hassle of even filing the paperwork.

Your gas mileage is about where it should be with the 31" tires. As for the *******, could try a tune up, filters, some injector cleaner. Sometimes this little stuff makes a huge difference in power. Check your Camshaft position sensor wiring, EGR pressure sensor wiring, and O2 sensor connectors to make sure they are seated properly and secure. An "intermittent" lose connection in any of these would cause your motor to lose power and be sluggish.

I had a similar experience with my cam position sensor harness. It had a lose connection that would go out randomly and come back, not often enough to throw a code but when it did go out I lost at least 30% of my power. Was a pain to track down.