Considering you have the complete motor and odds are the PI Motor has less miles on it i would just swap the motor IMO its easier then trying to do heads and an intake while the NPI motor is still in the car.And then you will have a better starting point should you decide to start throwing bolt-ons at it.
pi swap hp > pi motor hp
but if you swap the engines, you will be able to do more things down the road. if this is the only performance thing you will be doing, id say go with the pi swap. (if there isnt too many miles on the npi engine.)