My thoughts.
These are not worth the paper they are printed on, but here goes. If you want the '99, do some checking. See if you can find out who the owner was and talk with them directly. Ask them for a history of the truck, problems, mods, repairs, etc. Take it with a grain of salt, but it is a starting point. Does the truck have any aftermarket gauges? If it does or has, bet on other mods such as fueling boxes or aftermarket injectors.
Look at the truck and see if you can tell if it has had a fueling box on it. Hard to tell. Take it for a test drive... without the salesman. Drive to the nearest Cummins shop and let them check the codes. Get a list of the codes and see what they mean. Also have them check the lift pump pressure. No less than 10# at idle is acceptable.
If the lift pump is showing good pressures, that would help my feelings a bit. Worst case would be the need for a new injector pump down the road and many of us have done that anyway. Anywhere from $1500 - $2500 installed is a good figure to bet on. It can be had for less... .
Is it an auto or manual? I would be less leary of a manual, but that is me; the most you would probably need there is a clutch.
I have a '99 that I bought new and have been very happy with it. I have 159,000+ miles on it and I have put 2 new lift pumps on it. I also put a new injector pump on it at about 136,000 - 138,000 miles. That is it.
On my injector pump, it developed a hard start condition when warm, but never showed any codes. The dealer fought with me and would not replace it under warranty. It finally got to the point this last summer that it might take up to 10 seconds of cranking when hot before it would fire. I got the feeling it was going to leave me stranded one day. I carried it to a reputable diesel shop and the diagnosed it as the injector pump. Installed a new pump and it cranks and runs now like it did the day I bought it.
Good luck with what ever you decide!
PS. I still have my '92 as well and I would not have anything but a Cummins for the cold weather starting ability. Any cummins will beat any Ford or GM diesel for starting on cold days and the Cummins has the simplest, most reliable cold starting system.
The lift pumps going out and the one injector pump are the only problems I have had with my '99 and I have had a EZ fueling box on it for over a year now with no problems.
Sorry for the long post.