Quick update:
I have decreased the power by altering the potmeter on the Y-motor stepper driver and it did the trick!
I didn't use the multi meter as recommended though.
I just removed the fancase from the electronics, rotated the potmeter slightly clockwise, moved the fancase back onto the electronicsboard and tested the sounds via a bedleveling Gcode.
I repeated this a few times until both X and Y motor sounded the same.
I am now printing in slow speed to check if the temperature issue is also fixed. Until now the Y-motor is even slightly cooler then the X-motor so I guess decreasing the stepper driver power solved all my problems. (well....regarding the Ultimaker that is!!! :smile:)
Thanks again for your help!