More than likely you had a weak lift pump and ran the truck below 8 PSI starving the Injection pump for fuel, as a result the injection pump is fried since it will start to "pull" fuel from the tank, through the dead lift pump and either burn up the pump due to excessive heat (the fuel cools the I.P.) or it burns up the circuit board. This is the weak point in this truck. As mentioned, get a fuel pressure gauge and check idle and WOT fuel pressure, if you are below 8 PSI at any time replace the lift pump with either a new Airtek pump (Oreilly's, the Original Carter is junk) or upgrade to a Raptor, Air Dog or FASS system. I just installed a new system on my truck (Raptor) took about three hours, incredible difference in power and I am pure stock, no box or anything. I run 15 PSI at idle, the lowest I can pull is 12.5 PSI and WOT. The new system will eliminate all the banjo fittings and upgrade to 3/8" fuel lines (Looks like you ran a water hose for a fuel system) and will keep the pump happy. While your at it, install the big line kit from the fuel filter to the injection pump, easy install and also a huge difference. If you have a fried IP it is anywhere from 900-1500 for the pump and about 8 hrs to install your first time, some shops will install for a decent price. The upgraded Fuel systems include everything needed and will run aroun 400-500, but you will not regret it when finished, the truck will be a like a new beast when finished. Good Luck.

BTW, don't go through Dodge for the I.P. try Midwest Injection, Vulcan Performance or even Blue Chip (Best on the market with upgrades, most expensive at around $1500) Pensacola Diesel etc, most of the others are in the $1000.00 range. The dealer pumps are expensive and often don't have the upgrades, all IP's on the market are rebuilds, they are not making them anymore, even the dealer Injection Pumps.