Attention: TDR Forum Junkies I have to answer more from having followed this board closely for over a year, more than from personal experience. With that disclaimer, NO, I don't think there should be a big difference between 99 and 01. The big change was from the 12 valves to 24 valves at 98. 5, so unless you had some rare 12V with a 99 sticker, or you bought a 98 that was still on the lot in 99, you should be seeing approximately the same performance. And even if it was a 12v vs. 24v thing, your performance should be up, even if your mileage was down. Based on that plus what you have said, I think you are right to suspect that there is a problem with your truck. I would say, before you spend money BOMB'ing, get the stock truck right first.
Others have given you several good things to check first, so I'll start with a long shot: Watch your rpms closely, and see if you can verify that your torque converter is locking up when it should. Once locked and at cruising speed, I don't think you should get any engine speed variation unless pulling a fairly good hill. I had an old Suburban once; one wire came loose, the vehicle drove normally but with no lock-up, the mpg dropped about 1. 5 mpg. Found the problem by letting a good transmission man take it for a test drive; he could tell right away by the feel that something wasn't right, but to me it all felt OK.
You might also want to check http://dodgeram.org/tech/dsl/troubleshooting/24v_trouble.htm
A couple of things I noted - one is the fuel vent cap, which sometimes gets left on new trucks, and can cause poor power (there's also a link to pictures of the location); the second thing I noted is that "weak lift pump" is the only item that shows up under BOTH "low power" and "poor fuel economy".
Once you've tried all these "do it yourself" things, I have to say, you simply have to find a better dealer or a good Cummins shop. Good luck, I know it is a lot harder to find a minor gremlin than something that just makes the truck stop running altogether!
