HPFP can pick up +20hp and +25 ft/lb on a stage 1 tune and even make gains on stock. I have seen stage 1 tunes with turbo back exhausts and an intake cause fuel cuts and missfires.
as a test, put the original intake back on, see if the missfire goes away.
If you want a HPFP I have some Autotech internals, new in the box.