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just following up on this- i got the correct diode pack (first shipment was incorrect part pulled by warehouse staff). I was really planning on working on the truck when the wrong part came in so i went ahead and pulled the 2 wire alternator plug out, sprayed it with electrical contact cleaner and put some dieelectric grease in there, did the same with the charge wire where it connects to the battery terminal minus the grease, and the truck has improved significantly since. i can actually count on one hand how many times the torque converter has unlock/locked since that weekend. i never ended up pulling the alternator and still have the new diode pack in the box in my glove box for now, i'll get around to changing it eventually because when i was towing this 5th wheel it still did the unlock/lock under load. now i have new issues last week just one time i was in a drive thru and i normally turn the truck off to be kind the the people wearing the headsets and so i can hear them, when i went to restart it, it didnt start up right away. you get so used to holding the key down for a short time i thought maybe i didnt hold it down long enough but when i held it in the start position it took like 4 seconds to start (normally this thing barely finishes the first engine rotation and its running) now jump forward a couple days to earlier this week, i hop in to go to work and it does it again only this time it took closer to like 8 seconds to start. next day, little bit longer. now today when leaving work it took like 15 seconds or more to start, long enough that the dinger actually dinged at me a few seconds before it finally started. with all this, for the first few moments after it starts it has a rough idle but smooths out. i noticed yesterday leaving work that my quadzilla isnt being utilized, i connected to it today on my way back into work and noticed im not getting a fuel psi reading, map psi is frozen at 2psi, apps position is frozen at 8%, but other things like egt, iac, ect, timing, all seemed to be reading properly or at least gave that appearance of believable live numbers. so, leaving work i connected my actual scan tool to the obd port (its an autel ml629), and through the scanner i am getting an apps reading, i can see the map changing (31 inhg to 60+ inhg depending on throttle/load), and i have a new code, a p1689 its raining and i lack a covered location to work on it so hopefully tomorrow before it gets hot i'll get under the hood and see what i can see. after some searching it looks like a p1689 can be a few things so i'll try to check out anything i can

Fuel pressure is controlled by a spring and check ball in the return port of the Fass. AirDog does the same. Now if you can find the right size washer you can shim the spring too increase pressure if needed. As for stability there is a spring mod I do. FASS and Airdog are known to push the checkball into the coil of the spring. So if you bend the last coil over 90° through the center this prevents the check from pushing into the coil causing pressure drop. One project ive gotta do is replace Thor's pressure spring with the new one and modify it too.

Finally got back on this project last week. I lifted the bed, dropped the fuel tank and verified no restrictions of any kind in the tank or fleece unit. I put it all back together and ran the truck with no problems, pump worked flawlessly. 17 psi @ WOT, 19 psi idle and cruise. Ran for about 30 miles . Basically there was nothing fixed and I ts working as t is supposed to. I’m at a loss as what could have been or is the problem. Thanks for all the help, we’ll see how it goes

With all this apart I now need to figure out how to make my SLT trim harness work with the base model harness. This will be very tricky. The base model does not have abs* my wiring/modules do, the base model doesn't have power windows, locks, heat and I want them - my harness has them, overhead console/light, etc... I 'm thinking the only real hold up on just completely swapping harness's is the brake's. There is a brake module in the 1/2, has 2 plugs going to it and its not the same as what the 02 diesel had, obviously. So if I swap everything I'll just be left with a brake problem and now ill have a constant light in dash. I'm just now thinking of the speedo, maybe it's the same? Ill have to change info in the trucks computer so it doesn't think there's still 4.10s in the rear etc. Man this seems complicated now haha, am I overthinking this, how much computer stuff will I actually need to change overall..... I got some thinking and figuring out to do. If anyone has pointers or some advice I'm all ears!

I'm still needing info/advice on what I will need to swap the auto into the truck. Like what wiring harness/plugs, engine to trans cables etc... Anything that my manual truck does not have and autos have, I now need going forward with my 1/2 ton cummins. I hope that explains it enough lol.

Wiring anyone??? Entire truck wiring harness...

It sounds like you found a good shop to do the diagnosis and fix. Your issue could have turned out so much worse. I am sure that you have a new found respect for a "water in fuel" warning. Good job following the right path for repair and thank you for posting the solution. John

Update for others’ benefit: I finally bit the bullet and hauled the truck to a reputable diesel mechanic after siphoning 10 gallons of clean diesel out of the tank. They told me disposal for diesel had gone from $0.10/gal to over $4 so I was going to save what I could! Bracing myself for the worst, I was actually happy the bill was only $1200! The truck has a flatbed and what they found was that the idiot installers used radiator hose for the filler tube and the rubber inside had deteriorated and clogged the screen in the tank. There are also vents on the top of the tank that were missing and so rain water was coming in that way! Wasn’t an issue for the prior owner because he used it infrequently and kept it garaged. So the tank was dropped and cleaned out, hose replaced, vents corrected, and the new VCA replaced again. Thankfully injectors and CP3 ok. The mechanic had just finished working on a similar rig with the worst fuel contamination problem he’d ever encountered. Guy had an aftermarket oversized fuel tank that had an indentation where the fill hose goes in allowing water to collect and for some reason get in. CP3, injectors and fuel rail all needed replacing plus more, I’m sure. Over $3k for injectors alone…I’m feeling very lucky at this point! Thanks for the guidance here!

Interior is out now... If anyone needs special pics or curious whats behind the dash- hit me up... Wiring is coming out slowly. Still not exactly sure if every single harness will need swapped or if I'll just do it all to avoid confusion down the road. Might rebuild the hvac box again, found that Genos Garage has a ac/heater box seal kit for $55 I might try instead of just making my own with peel and stick foam tape-pita.... Found a 2003 1/2 ton disc brake axle for $300 I might get to change the rear over to disc's. You only have to move the spring perches in just a bit apparently, well see lol. Its coming along! Wish me luck! **Still needing insight on what else I'll need swapping over to auto from manual... surely wiring and more?

been a busy summer doing other things, but things are still moving forard...just slowly...