You shouldn't see any smoke with a stock engine except at startup. I'd be concerned with possible cylinder wash and engine damage. An 02 is still in warrenty and you should get it into your dealership for peace of mind. If at any time they say "that's normal", run, don't walk, out of there. The standard charge for this kind of service is around 100 bucks. There are many things that contribute to ill running diesels. The problem is with diagnostics. Unless you have a shop like Piers next door your best bet is a local Cummins shop. Fixing the problem is only part of the battle, finding the problem is the key, don't accept; it SEEMS normal, there is nothing on the scanner, I can't get it to repeat the symptoms, they all do this!
I don't know where you are but I'd be willing to help with an injector install, it is another step that we all take. Mike