Hi there!
If the midi crackles it might have many reason. First know that when I've started my Stormmedia Final Fantsy Sound project(a soundfont with very good quality insturment) I was using a softsyth that use SoundFont. But my SoundFont was too complex for this program and my CPU usage was considerably high resulting to many bugs in the music(crackles) that started only at some parts of the music. So I think the problem might be an overload of your CPU. I don't know what could 'cause it though ... unless you use a SoundFont very complex(like mine) I think your machine you shouldn't have problem to play midi.
Well it might be a graphic car problem too since you say that the the graphics start shaking slightly. Did you try to use software render? maybe the game has a compatibility problem with your graphic card and the game try to fix the problem using the prossessor witch could explain the CPU overload.
Well give more detail about what you are using to play this game(setting, Midi driver, SoundFont, etc.).
See you!