I missed this thread the first time around.
I'm getting out of the welding business
What!?

What in the world possessed you to make this decision!? Obviously you're not thinking clearly. Is now really the best time to make a major truck decision?
So, I should count on putting in FASS (or similar) system to replace the stock filter location lift pump and also a better fuel filter, right? Would a fuel pressure gauge also be recommended then, or will the FASS make that redundant. The truck will remain at stock power levels for quite some time.
If the truck still has the lift pump mounted to the back of the fuel filter canister, you'll need to plan on changing that out with something else. I also think that a fuel pressure gauge is a good idea, even if the truck has already been retrofitted with an in-tank pump. It's just good cheap insurance.
Many of us also run supplemental filtration, in the hope of staving off injector problems. No one really knows how effective it is, but it makes us feel better.
the 12v's will always reign supreme for reliability, power per dollar, etc.
I've never been in a 12v, but I agree with Forrest on this. You can't beat a 12v engine for durability and bulletproof-ness. If I were in your situation, I probably wouldn't move to a HPCR truck. Just my personal opinion, but I figure I can spend a lot of time and effort fixing rust and paint before buying a new truck becomes a good choice. But my priority is usually on mechanical reliability rather than aesthetics.
As mentioned, the biggest problem area is injectors on the HPCR engines.
Aside from that, we see lots of problems with bad universal joints and bad carrier bearings causing vibrations.
Fan clutches also seemed to be a problem on some 2003-2004 trucks.
Very common to have a blend door break (even up through 2006, I think), so you'll want to check the HVAC system to see that it blows air from each vent as it's selected.
Water pumps seem to go out between 75k and 100k, possibly due to sand in the block.
Very early 2003 and 2004 trucks had vibration issues caused (apparently) by the power steering hose that runs to the hydroboost unit. There was a TSB that replaced the hose with a weight to dampen the vibration a bit.
There was a problem with the fan clutch wiring harness rubbing a hole in the radiator! Many people had that problem.
Link.
A lot of early 2003 trucks (2004 too?) had low axle fluid levels from the factory. I assume this would have been fixed by the time you get to a used one, but you never know.
2003 and some 2004 trucks had a problem with the clutch making a knocking noise in neutral with the pedal released. This was fixed by a TSB that replaced the pressure plate, I believe. The knock won't hurt anything, but many people found it annoying.
There was a batch of trucks (mine was included) that had a paint issue from the factory. Many of us got letters direct from PPG that provided a 100k mile 10-year paint warranty. I assume that any afflicted trucks would have peeling paint by now, so this should be an obvious one to diagnose.
Speaking of paint, many 3rd gen owners used to complain about very thin paint, and a lot of discussion centered around people trying to get the dealers to repaint trucks. Some were successful, most weren't. Thin paint issues show up more on the darker colors, because the primer is white. [My truck actually has areas where paint is MISSING!].
Early 2003's had an alternator bracket that would crack. This was replaced as part of a recall. Check the alternator bracket - the crack should be obvious. This was an early 2003 problem only (pre February 2003).
There was a problem in 2003 with the "check gauges" light flashing intermittently for no reason at all. I think it was fixed with a computer flash.
There was also a problem with a slow fuel gauge response after fillup. It was fixed by the same ECM flash as the one for the check gauges light problem. I never had the flash... I just live with the slow fuel gauge response.
Occasionally the 2003 trucks would give a "blank stare" out of the overhead display. It'll read "--", with no way to reset it until you shut down and restart. Computer glitch - nothing to be concerned about.
Very loud AC compressor clutch when first engaged after sitting for awhile. An intermittent problem that will make you think the compressor just exploded. Very loud. Not an issue (mine has been doing this for 76k miles now).
Don't forget the front hub bearing assemblies! If the truck lived in a salty environment they will be electrochemically welded into the steering knuckles, and impossible to remove without destruction and a whole world of swearing.
Link.
I still believe, however, that the 2003-2004 trucks are the best of the HPCR series. I base this opinion on the complete lack of emissions equipment. The fold-flat load floor is nice on the 2003-2005 trucks (the 2006-up load floor is pathetic). I also like the tie-down cleats in the bed of 2003-2005 much better than the little rings they started using in 2006.
My goodness, that's a lot of words.
Ryan