Dorien,
The MotionChart is not very customizable in the way you are hoping, but it sounds like you could make use of the Bubble chart with the animation option which you would control to synchronize with your music. For each animation step you would just change the data and set the animation duration and call draw() again. You could add a Pause button that just interrupted the process, though the last animation step would continue until it was done.
But the animation times are likely to get out-of-sync with the music unless you can get some signals from the music itself. Another alternative might be to chop the mp3 into many small segments of known duration, and play each one successively.