To me it sounds like your engine has been heavily BOMB'd even though the boxes are off it now once you add the Boxes it is your warranty from that point on.
I have seen many guys spend days removing there BOMB's just so that they can get warranty work done, which in my opinion, was directly related to there BOMB's and or racing or sled pulling abuse. There is no doubt this is complete fraud, and with the dollar amounts caused by the fraud it may well be a felony.
I can't understand how people can modify these trucks way beyond stock and expect other owners to subsidize there play?
There is no way a stock Cummins needs a blow-off valve and any dealer knows that, as to what caused your engine failure I can mostly likely say it was caused by your need to have more ponies under the hood than your buddy, when you push the envelope you better be ready to pay!
When I bought my 03 back in Dec of 2002 I was told that even oversized tires air intakes and or large exhaust would void the DC "powertrain warranty" that was at Dave Smith Motors in Kellogg, Idaho.
The best way to get your truck running if you are completely strapped is find a wreck motor on ebay or elsewhere and find some friends to help you get it running again try your local chapter of the TDR for starts.
I feel your loss and I am not trying to through salt in your wounds, I have done some expensive dumb mistakes in my life. The fact you shared your story will help others gauge the risk when you feel the need to Modify your truck.