I've had aftermarket CAI bog down in the 1500rpm range off the line in a MAF-based subaru. After going through several iterations, I found that keeping stock intake but gutting the intake muffler, and even using alumized insulation wrap, still using the factory opening, which was usually CA from the grill/bumper, yielded best of both worlds. Snappier response, growl at deep throttle, but no bogging. In my case, the subaru never could relearn the CAI.
One theory is that the factory intake usually has resonators in them-- I assume they are to kill noise, but they may also be there to kill "noise" near the map or maf. without those resonators there may be some confusion for the sensors.
I am more prone, in your case, to agree that the more open exhaust has dropped your back pressure some and you are feeling the resultant loss of torque.
Mike