Transmission Issue

Hey guys!

I'm new to the forum, just joined today. I have a 2013 Tacoma TRD sport with a 5-speed auto transmission. In terms of powertrain modifications, the only thing I have is a Volant CAI with ram air system, 100k mile filter included. Additionally, the Toyota place also installed Flowmaster Catback exhaust. These modifications have been on for several thousand miles, and it currently has around 41,000 miles. The transmission shift/engagment from park, reverse, drive and neutral are all typically smooth with a few hiccups when the engine is cold. My major concern, however, is that with no temperature dependencies, in the higher gears, will not want to shift and when it does, the RPMs shoot up over a thousand RPMs from what it is originally while shifting is underway. Also, I have noticed a slight decrease in gas mileage, I usually get 19-22 hwy, but currently struggling to get to 19. It also seems to be running more RPMs than normal in lower gears.

If any of you have any ideas, it would greatly be appreciated.