Don't hold the clutch to the floor when you slow to a stop. Put the car in neutral and let the clutch out or downshift. If you are not pushing the clutch in and it is still doing it, unplug your batter and turn on the headlights. After a few minutes plug the negative of the battery back up. Drive it for a few days and it should learn the new filter and work fine. Mine stalled once after installing the K&N FIPK but never has since.
I just installed an accufab throttle body and plenum the other night and it caused the same thing. High idle and stalled a few times. After about 600 miles it has learned and the idle is back to normal and no stalls.
-Jason