you shouldn't have a loss of power from taking off that ridiculously restrictive stock one. i'm not sayin you should have felt a HUGE increase in power...but definitely not a loss. I hope you just didnt have high expectations for adding a CAI and exhaust..so now if feels worse even those its just that nothing changed. they are good for sound and that's about it.
if it still bothers you then looks like u gotta go to and through exhaust like magnaflow. I have the flowmaster 40 on my truck and didn't know a loss at all. and it sounds amazing.
how long ago did u do these changes?