I'd replace the under hood power distribution box computer & fuel pump power relays & the in cabin fuel pump inertia switch & drop the fuel tank & clean it out for sure.

 

When I replace the fuel filter on friday I'll check it for debris. If it has chunks then I'll drop the tank and clean it out. Found a rebuilt PCM for $130. Autozone has the inertia switch in stock I think for about $35. I'll replace all the relays when I get under the hood when I'm cleaning the fuses. Juggling this truck issue with repairing the sewer lines in one of our rentals so I gotta balance out the time.

 

Pulled the fuel filter today and not a spec of debris. Good pressure on both sides. Stopped to get all new fuses and relays for under the hood and a inertia switch. Autozone had everything but the relays so I'll check some other stores this evening when the wife drags me out grocery shopping. Wrench guy had it up on the rack for the fuel filter inspection, spent maybe an hour futzin with it and didn't charge me a nickle for his time. I tried to pay him but he said nope, you'll be back for other things in the future. He's right of course. He did suggest a complete tune up. I checked the photos on how high the water got and it didn't reach the computer so that's good news. Now to replace the fuses, relays and inertia switch and see if that makes a difference.

 

Ok good to hear the new fuel filter isn't full of debris. I agree with replacing the under hood fuel pump & computer power relays & the in cabin fuel pump inertia switch, as those items were under water, aren't sealed, so are likely silted up & maybe rusted/corroded internally, so their electrical contacts are highly suspect of being corrupted from rust, corrosion & silt, not good for those circuits.
Have you had the under hood computer firewall electrical connector apart to see if the water & silt got into it? If it did, use a good electrical contact cleaner like those mentioned earlier, with a tooth brush & tidy up as well as you can & spray them with a good quality silicone spray, like the CRC Heavy Duty Silicone Spray product. All under water electrical connections belong on the suspect list & that includes the battery to engine & body & body to engine ground connections.
Remember Electron flow is from -/Negative to +/Positive, so those ground connections need to be clean, bright & tight, as well as the B+ connections between the battery to the under hood power distribution box & alternator, to keep our electrical system happy.

 

Got the fuses and inertia switch replaced now. I just gotta find the relays to replace those. I'll clean all the ground connections as well since I'll be under there. Water didn't get high enough to reach the computer but I'll clean the connectors out anyway. It wasn't submerged but I'm sure with enough moisture from sitting in the water there could be an issue.

 

Found the relays at another Autozone and was talking about what Little Red was doing. He suggested I try a new fuel pressure regulator. I looked them up and there was a review that sort of described what my truck is doing so I'm gonna go ahead and replace that too. The regulator is on the fuel rail so I know it was under water.

 

Successful test ride today. No cough, no hiccup, no sputter. One of the plug wires had been rubbing up against one of the metal tubes down there on the driver's side and it was chaffed to the point of exposed conductor. Every so often it would arc to the tube instead of going to the plug. Changed out the plug wires today and so far smooth as jello pudding. When I went up to the shop today to talk about maybe the injector connectors being corroded and how easy it is to get to them the wrench guy came out to see. While he was under there he found the chaffing and moved the wires around a little. I noticed that after that the sputtering was gone so up to the parts store for new wires. I'm certain the shop that initially fixed the truck after the flood didn't change out the wires like they said. I rerouted the wires with the clips so they are a little easier to access and they don't rub or touch anything. Gonna take the truck to the next town in a day or so and see if this really did fix it. Tomorrow is a busy day up in the city and we'll be taking the Jeep.

 

Ok good find & feedback on the plug wire rub through & replacement seeming to fix things such that its running smooth now.