Well, I've had my truck since last May '01 and since then I've done this to it:
Dumped the downpipe under the cab - then went straight piped, removed silencer ring, took plate out - and adjusted AFC, installed gauges, installed Piers' governor springs (best mod thus far... ), redid my transmission lines with 1/2" double braided hydraulic hoses, rear main seal (it was leaking when I bought the truck), two transmission fluid/filter changes, front/rear diff and transfer case fluid changes, two front calipers, a set of brake pads, killed my KDP with CPFF's jig..... and that's about it.
This is a daily driver and I've put about 30,000 miles on it since I bought it. Notice how most of the stuff I've done is elective surgery... .
The alternator is a stout unit... and readily available/rebuilt... . the same goes for the water pump (you mentioned it twice... )..... by not having the engine cooling fan beating the crap out of it... it lasts longer... . plus it's easy to change. The wheel bearings are a pain in the butt to work on... but mine have been okay... . same story for the ball joints... . and all of the steering components.
Keep the fluids clean, don't beat on it like a rental, and everything should be just fine.
HTH,
Matt