Change stock Clock app timer noise?
I've got the same problem and the annoying sound can not be found in /System/media/audio/, but in /system/app/DeskClock.apk/assets/sounds/Timer_Expire.ogg. In any case, it seems difficult or impossible to change.

There is more info here: 
http://androidforums.com/nexus-4/668411-super-harsh-countdown-timer-sound-nexus-4-how-change.html