Check your clutch slave cylinder and make sure nothing is obstructing it from operating properly. It is located at the front of the transmission there may be a wire harness or something close to it getting in the way same thing for the gear shift mechanism on the transmission when you change gears there is a mechanism on the transmission you can see it from the top it will move when the gear shifter switches gears. It is on the right side of the engine a little bit left of the battery. You need someone to sit in the car and shift through the gears while you look under the hood you will see it move. I have seen aftermarket cold air intakes get in the way when they become lose or a vacuum hose that goes into the side of the CAI.