Window: if you're hearing the clicking under the dashboard, it's a bad resistor. If you're hearing the clicking in the door itself, either the motor is locked up or the tracks are jammed up. pull the panel window motor and check the power supply with a multimeter. if you're getting 12 volts when you push the button, it's the motor. you can check the ohms on the motor itself but I always just get two pieces of scrap wire and test the leads on the battery to see if the motors even turning.
Whistling: Throttle body spacers - in my experience do very little and on newer vehicles can freak out your whole system from TPS to Cam and Crankshaft position sensors. That absolutely could be causing the whistling or if you have an aftermarket cold air intake - those make whistling sounds too.