Some good information in this thread already, but also a few things to clarify.
With the modifications installed, the truck should have no problem running on the stock tune. On certain vehicles, tuning can be required after installing simple modifications like an intake - these are 99.9% of the time going to be vehicles that use mass airflow (MAF) sensors (ex: Subaru EJ and FA platforms, R35 GTR). The Raptor
does not use a MAF sensor to calculate airmass entering the engine, and instead uses a speed-density method that uses manifold pressure (MAP) and air temperature data (among of a few other variables) to calculate airmass at any given operating condition. Speed density types of airflow measurement systems are generally unaffected by intake changes. The only DTC that you may see when installing certain intakes on Raptors is P04DB which is a crankcase pressure fault code. The PCV system has a pressure sensor used to detect when hoses may be disconnected or leaking to meet emissions standards. Depending on design of the intake, the crankcase pressure sensor may read outside of its acceptable pressure ranges and throw this DTC even when the PCV hoses are connected. Even if this DTC was present because of the intake installed to your truck, it will not be the cause of the misfire.
For more information on why tuning for a MAF vehicle is important and some of the differences between MAF vs. MAP based airflow measurement systems, check out these links:
As FordTechOne mentioned, a flashing check engine light will indicate a misfire. By far the most frequent cause of misfiring on these engines is going to be spark plug wear and tear. Even though the previous owner claimed that plugs were replaced recently, improper gapping or improper gap adjustment techniques (and related damage to plug) could explain the misfire. Replacing them with new set of MotorCraft or Ford Peformance plugs is a cheap and easy test (this is not a spark plug swap on an old Ford 4.6/5.4 Triton where they break off in the head half the time, ask me how I know...)
Whether you plan to tune or not, COBB OTS maps are designed to operate on stock plugs with stock gap, so the MotorCraft plugs are fine to use.
Still,
it is always important to scan for any engine codes that are thrown when either the check engine light or wrench light turn on - there could be other codes that are contributing to the misfire condition like a stuck wastegate actuator, overboost condition, malfunctioning variable cams, or fuel system malfunctions. Any scan tool will work, you can get a cheap one off of Amazon for a few bucks, drive over to the local Autozone/O'Reillys/etc and borrow one for free, or use an Accessport!
Let us know if you have any questions and what you/your dealer find with the truck. Best of luck with the new purchase.
-Sam@COBB
