Doubleup,
Hope everything is back to correct at this point. Here are a few suggestions from a mechanical & electrical view.
Headers are pretty much academic as far as installation goes, but the Viper does require the removal of quite a few body panels, engine bay components and electical connections. Here is a quick check list.
(1) Always disconnect your battery
(2) Check spark plug/coil wires for damage ( possibilty of being pulled apart?)
(3) Spark plugs for cracks ( not neccesary to remove during installation on Gen IV )
(4) O2 sensors plug ins & connections ( use thremal tape to insulate )
The lower intake is staight forward but requires removal of Key fuel & engine management sensors.
(1) Always disconnect you battery
(2) Check your fuel injectors to make sure completely seated in intake runners
(3) Check fuel injector ignition connectors
(4) Fuel Line connection
(5) Vacuum connections
(6) Coil Connections
(7) Intake bolts to ensure factory trq spec
(8) Fly By Wire connections
(9) Fresh air intake secured ( no air leaks )
(9) NACA Duct air deflector must not be removed
(10) If running a MOPAR Performance Controller ( unit must be installed correctly using a "Specified Sequence and Check List". MJ from WoodHouse Motorsports posted on a previous post about this procedure. I recommend good reading for all ).
Don't hesitate calling my cellular is on and honestly the headers are not going to be the problem its a sensor, connection or sequence issue most likely.
Here to help
Toddy