I have a '98 2500 quad cab short box cummins 5 spd. I love driving it.
It has 3.55's (which I will shortly discard for 4.10s to help the 35's) I have a 53 block, no problems to report with the block. But I am stock power level. nv4500 5 gear nut is known to backoff and you lose the use of OD. Design of the splines on the shaft, there are fixes for that. It backs off usually due to lugging the cummins in 5th. Check out the front end, they are known to get loose. track bar and steering box. And fuel transfer pump, as I just found out on mine, are in a crap location for an electric pusher, and fail often. If undetected soon enough it will take your injection pump with it. Ask about it, put a guage on it during inspection. There is a 1/8th" NPT plug on the top of the fuel filter you can use to check transfer pressure, IF there isn't a fuel pressure guage installed already. The nv4500 MUST has Syntorque oil in it or the syncros will fail prematurely. D60 front, D80 rear....... what else...... Like I say, can't complain, I love the truck. I will get a newer one someday, and it'll be a dodge.
3/4 & 1tons have different sized tanks IIRC.
Oh and the NV5600 when introduced in '99 till '01 have a known weak input shaft. It was redesigned in '01. Skip those 6spds get an '98 or '02-newer for stick. I'd stay away from autos all together, but thats just me.