You should check out Keith Hamel's Notability Pro. (http://debussy.music.ubc.ca/NoteAbility/index.html) Its a notation program that includes score tracking and full integration with Max/MSP. The score will do its best to listen and follow along and you can place various Max events in the score to control a Max/MSP patch to do your processing. It is something I have been meaning to delve more into but you will need to contact Keith directly via his website if you have any more questions. I have only seen Keith and a few others use it here in Vancouver and not actually mucked about with it myself.
The only "hold up" is that I like to notate my music and max/msp doesn't
have notation. If it would run as a VST plugin, then I could manage the
Notation on the Cubase side and the processing on the MAX/MSP side.