"I know where there might be one of these trucks for sale: it's a 2000 3/4ton, 4x4, cummins, auto, extended cab shortbed. Sport, power windows and locks, air, cruise, tilt, cd player and cassett, bed liner, tonneau cover, nice wheels, and a set of buckshot 285's. Truck has ~45,000 miles on it. Body and interior excellent. No leaks. My questions are: What is it worth?"
I traded my 2000 3500 QC 4x4 with 56K miles in 6 months ago and they gave me $23,000 trade in value (plus my truck had $3000 in hail damage on it) I would think that the truck you described would be worth $24,000 from a private owner.
"How troublesome will my injection/transfer pumps be?"
I had the lift pump replaced on my 2000 under warranty at around 45,000 miles. On the 2000 the lift pump is covered under the 7 year 70,000 mile emissions warranty, not the 5 year 100K mile engine warranty (different years have different coverage, need to read the book)
"How about the auto transmission?"
The automatic transmission is covered under the 3 year 36K mile warranty for the 2000 model year. As long as the truck has not been abused or the power turned up the stock auto is a solid unit.
"What will mileage be?"
It depends on the rearend you have in that truck. My 2000 with the 4. 10 got 16 mpg around town and 19 mpg on the freeway. My truck weigh 7200 lbs stock. I would think the one you are looking at would get 18 mpg around town and 21 mpg on the freeway.
"Is the warranty still in effect?"
Before you buy this truck from a private owner I would take it to the dealer where you will have your warranty work done and ask them if the trucks 5 year 100K mile warranty is in effect, have them look and see if it has ever been modified. Then get it in writing that the warranty is good from the dealer. (just a note on the work order from the service manager will do) After you buy the truck there is a number in the warranty book that you call and give them your name and vin number and they will transfer the warranty into your name. They will also put you in the system for recall notices etc.
"Is the KDP an issue with 24 valves?"
Like Justin said KDP is not an issue for the 2000 and newer CTD's.
Just for grins you might want to check and see what block it has in it. If it has a #53 under the VP44 and right above the oil pan it is not a problem but you can use it to lower the price. The #53's had a 6 mm thick block instead of a 12 mm and some have cracked below the exhaust manifold and above the oil pan on the passenger side. If there is no #53 in big 1 inch letters cast into the block then that is a good thing and means you have a Mexican block. ( don't tell the seller

)
Good luck.