Bernie above addressed it but I will emphasize the point about a modified used truck. If I were buying a late model Dodge-Cummins I would go to great lengths to ensure I wasn't buying one that had been modified. It is apparently very common for the youthful or uninformed to add electronic black boxes and run the truck hard for a while then when the problems begin developing (which they will), or worse, after failures have occurred, the owner dumps the truck on the used truck market. Electronic black boxes cause injector failures, at high power settings the failures seem to occur quickly. Injector problems cause piston failures, dropped valves, damaged top piston rings, and generally overstress the engines. New engines are very expensive!
Another thing to avoid very seriously is modified or aftermarket air intake boxes or aftermarket filters. They allow dirt particles to pass and cause accelerated engine wear. Yeah, I can already hear the squeals of outrage at this statement. But several recent threads prove it as did Joe Donnelly's testing reported in TDR magazine several times over the years.
If I were considering a particular truck I would pay a skilled dealer tech, one with a suspicious mind, to run the diagnostics and physically examine for evidence of tampering. I would never buy a used truck that had had aftermarket engine performance accessories installed. Never.
I disagree with Bernie's comments about the choice of transmissions in Gen III trucks. The NVG-5600 I had in my '01 behind the HO engine pulling heavy trailers held up very well until it suffered a bearing failure at 302,000 miles and was inexpensively rebuilt. The failure was encouraged or caused by my allowing the transmission lube to get a little low. Overfilling is recommended.
OTOH, the German designed Brazilian manufactured G-56 is an all aluminum case, less robust than the American made NV-5600 and is used with a trouble-prone dual mass flywheel. Early versions of the G-56 had poorly matched gear sets for the American application. They were geared too low. For model year (MY) 2007, the G-56 was delivered with slightly higher ratios in the lower and top gears. Several TDR members know how to identify the difference and have posted the two letter designation here.
I do agree with Bernie about the 2006 or 2007 being very desirable trucks. The last two MYs offered the best electronics (except for the reverse/door open alarm on 2006s), the highest power ratings, and several nice features like programmed fast idle in cold weather, slightly better styling, and improved headlights.
If you are determined to buy a manual transmission, I would prefer a 2004. 5 or 2005 with NV-5600 over the G-56 w/ dual mass flywheel/clutch assembly. My overall preference would be a 2006 or 2007 w/48RE and Jacobs exhaust brake.