No personal experience, but i've heard more bad than good about procharger in the mustang community. To rule out the procharger, disconnect it and return the engine to stock induction, leave everything else the same, and see if the stutter problem is still there.
Just thought if this, was a custom tune done to the computer when all these upgrades were added? You can't just bolt on a bunch of things and expect it to perform. All the engines performance parameters will need to be changed with a tune, preferably at a shop that has a dyno to perfect the tune.