Dad has an '01 HO (505tq rating with the 6spd). ~240k on it now.
He still runs the stock-style lift pump, and has had a couple fail. He carries a spare LP under the back seat; they aren't very hard to deal with, even in a parking lot or on the side of the road. Still has the factory IP-VP44! A fuel pressure gauge is a good investment to watch for a failing/failed LP.
For a replacement LP, there is an in-tank retrofit from Dodge (good), FASS or Raptor (better), AirDog (I would avoid personally, too many complaints read on CumminsForum).
The 6spd manual is the best way to go!!! The 5spd man trans has gear ratios that are just a little too spread apart. The 6spd closes those gaps and is a much better towing trans.
Dad has had Edge-EZ to boost it to ~600ftlb since around 60k miles. Woke truck up, pulls almost any hill in 6th (3.55 gears, 4wd, stock size tires) at 20k gross weight.
His is a comparable in towing to my 3rd Gen (see sig) truck. The 6spd really makes a difference in towing abilities. My 3-4 ratio gap is huge, and that is where his 5th gear fills that void. I wish I could have found 'my' truck with a manual trans...