I noticed the same thing after I installed my intakes and cbe. I didn't disconnect the battery when I installed them. After about a week I decided to disconnect the battery to reset the ECU completely. After about 100 miles or so, the power loss I experienced was gone and all was good again
I also have a theory that some of the power loss "felt" is somewhat in the mind. When you're used to the sound of your car at certain RPMs and all of a sudden you go install intake/exhaust, I think you need to give your brain some time to adjust as well to the new sound per RPMs if you get what I'm saying.