For the clutch, the pedal needs adjusted.
This is for a DSM but works the same on a 3/S
as far as the beep though, there is nothing related to the engine or drivetrain that should or would beep in the car.
Your best bet is to return the car as stock as normal as far as things that can affect how it runs. blow off valve, tuners, etc. and start from there.
Get yourself a boost leak tester and perform a boost leak also. That can resolve a world of issues.