I dont see any reason why the IAC would be acting up if he didnt touch it during the tune-up. Then again its the stuff that coincidentally breaks while working on something else that leads to difficult troublshooting that we all hate.
OP, Did you disconnect anything from the airbox while installing the filters? IAC hose/ IAS sensor. Doublecheck all is attached.
Also, did you disconnect the battery while working on her? If yes, it is possible your ECU/Throttle posistion sensor will have to relearn WOT and how to idle.
I think you just have to turn the key foward one click (not starting the motor) and push the throttle down all the way a couple times to tell the computer where WOT is. As for the Idle it takes alittle while of normal driving and idling for the computer to determine the exact posisions of the IAC to be in diff situations to idle properly
goodluck and keep us posted