[Big Dave]

Interesting case. An exceptionally poorly maintained truck.

Yeah, having been run out of fuel on multiple occasions may have damaged injectors. MPG will be poor until you address that.

Your idle GPM is unusual. Is your EPBV stuck closed? Mine gave me fits so I electrically disconnected it so it never closes. It takes longer to warm up in the winter but gaining 2 MPG in winter is worth it. The EBPV is essentially an exhaust brake. Mine stuck closed from September til May.

Also you may be idling too fast. Mine idles at 750 RPM.

Your junk yard engine control unit is doing you no favors. If you drive enough for MPG to matter you need to address this.

Lowering the truck will definitely help your MPG, but I know of no commercial kits for lowering a 4x4. I lowered mine 4" in front and 6" in back but my truck is a 4x2.

A tonneau will definitely help. For me it gained 1.5 MPG over an open bed. If $300 is too salty, go buy some 4x8s of plywood and make one yourself. there are a boatload of guys on this forum who have made some really effective aerolids for pickups. When bondo starts making aerolids I intend to buy one - the wind tunnel says his lids are the gold standard of smooth air flow on pickups - and I'll sell my A.R.E. tonneau.

I have nothing to offer on an automatic. Before my F350 I had a GMC diesel with an automatic and after seven trashed trannies I said never again. In my view all automatics are trash. Complicated. Expensive. Frail. Inefficient.
I have 287,000 miles on my truck and I still have the OEM clutch in it.