Oops, I just noticed you have a magic black box in your signature. That changes my recommendations. I simply have no idea what may be wrong with an engine that has run a magic box. I don't use them and have zero experience with them. Use of the Smarty box may have caused damage to one or more injectors or other components.
Several TDR members become angry everytime I express my opinion about magic black boxes but here it is anyway: Adding a box to enhance performance alters injector timing and rail pressure. Either one of those alterations creates an operating environment beyond that the engine was designed, built, and tested for. It is, in my opinion, a risky thing to do.
I believe the injectors in our engines were designed and manufactured to perform reliably for several hundred thousand miles under factory stock conditions. When you alter injector timing you alter compression pressures, sometimes significantly. IMO opinion, the factory injectors are fragile if subjected to magic black boxes.
As far as I can learn from TDR member comments, all magic boxes increase rail pressure. The factory injectors will not withstand higher rail pressures with the same reliability and durability as they will factory design pressures. In plain language, magic black boxes cause injector failure. Higher rail pressures cause the tips to crack, split, or break.
You have a problem with taking your truck to some dealers because of the black box. If they suspect the truck has been modified or "hotrodded" and you're in complaining of an engine issue under warranty they will be less cooperative about any and all warranty diagnosis requests or repairs. If they run any diagnostic tests on the engine they can detect presence of a magic black box, even one that has been removed. A sharp dealer tech knows how to find the trace evidence. Your warranty is void now anyway.
So, you have a problem! The way to solve your problem is to repeat after me, "I modified my truck, I am my own warranty company. " Once you accept that fact, your problem is reduced and the solution becomes clear.
Take your truck to a good, honest dealer service department with at least one Level IV trained and certified Cummins tech and acknowledge the former use of a black box and ask him to run the cylinder performance test at your expense. The test will measure and compare the power output of each cylinder. A weak injector or other component will show up under this test. If he finds a problem, get out your credit card or check book. If he finds nothing, maybe you are lucky.
I'd still PM Mike Mullenax and tell him the truth and ask for his advice.