First off, welcome to the forum, and congrats on having such a rare truck! Technically, the crew cab C3500HD did not even exist, but a few big buyers, such as Union Pacific were able to get them bought. They were not in the brochure and a regular small order buyer could not get them.
check and see what rear end gears the big girl has, it will either be 4.63 or 5.13.
I have been doing some small time hotshotting with 6.5Ls, and have had excellent luck, alot of which I credit to the 5 speed manual. The 4L80E is pretty strong, and many have good luck with it, so I would not swap just because. If she goes down, I have long pondered a Allison swap, and the HD should have more room underneath to get it to fit.
Take it from someone who just burnt up the engine on a 93 K2500HD with the factory turbo. You wont get along well with a factory turbo unless you baby it.
Also, another thing to keep in mind with the big HD is that there will need to be modifications made to whatever exhaust you install, as the down pipe is longer. So basically buy a Diamond Eye, but you will need to mod the down pipe.
So, If I were you, I think the smartest route would be:
Fluidampr, and a fresh damper pulley (and crank seal of course)
Diamond eye 4 inch exhaust
A-Team Turbo
K47 air box or S&B (absolutely do not go with a cheap "CAI" as most of the time they are the opposite, a hot air intake)
99.5-00 (order for a 2000 model year C3500) water pump and fan clutch, and a 01-04 (order for an 01 to be safe) Duramax fan. Try to go genuine OE grade AC Delco on the WP at least, and preferably the other parts as well.
The rear end is a Dana 80. I would order a Mag-Hytec Diff cover for it and some 75w140 or 85w140 synthetic gear oil for it. It has a slight flaw in its design, and is pretty hard on oil. GM recommended changed the 80w90 every 3K miles, or 75w140 synthetic ever 30K miles. when shopping for the diff cover, it will commonly be referred to as a dodge application. The axles are quite different, but the center section has the same cover pattern so dont be worried ordering a dodge dana 80 cover for your GM dana 80.
Also consider a deep pan and synthetic oil for the transmission as well.
Check over the disc brakes, rear discs are a little high maintenance IMO. Make sure your parking brake warning light works, quick way to cook the rear seal out of the transmission if you forget and leave it on.
Past that, maintenance is the biggie, I like to fairly quickly get stuff switched over to AC Delco professional grade USA made greaseable u-joints, and physically remove the radiator and clean everything.
For engine oil, I run Mobil Delvac 1300 super conventional grade, and once I find a vehicle that does not allready have oil leaks, I will be switching to synthetic.
many seem to be quite happy with Amsoil.
As far as parts sources, mine are: Leroydiesel.com (owner of the business, Leroy himself, is username Burning Oil above) a good local GM Dealer (buddy up to one, should be able to get 15 percent off if you are a good customer, also a good one will be VERY helpful looking up parts) ebay, amazon, and rockauto.com.
Also, this is one of the top 2 6.5L diesel related sites, so you are in good hands.
There is one, and only one 3500HD forum, at what other address than
www.3500HD.com.
It is good info for HD specific stuff, and guys can help find HD specific parts. not very high traffic, but they are all still actively posting.
A word of advice, keep track of expenses, try to squirrel away $ for repairs and upgrades, and track mpg, and most of all, try to get high $ loads, as hot-shotting is not usually a huge money maker.
Good luck!
