I remember reading about the flash when it first came out & from what I remember the flash did nothing to the fuel delivery. It only advanced the timing a few degrees, so why would the FPR kit be bothering anything? The car is still going to run overly rich & FPR kit should still be doing its job.
My car is not running higher boost right now, but I still have the FPR kit on after being flashed & the car runs great.
I say reset the computer & go from there, also why take off the FPR kit, I mean dont you now have to plug the hole you made for it? Especially with the Injen intake.
I also thought getting colder plugs was best if you are boosting past 10psi?
So if I were you, I would reset the computer first then if the problem is still there, change back the stock plugs. The hesitation could be that the colder plugs are not doing the job of fully igniting the mixture, maybe.