I've been trying to figure out some way of using interactive music myself. Not really what CrudeMik is talking about, but something similar to guitar hero just for a platformer.
I recently downloaded that huge file thats supposed to let you make plugins even with VC++ Express. I fiddle around with synths too so hoping I can program something to include a VST. (I know very little C++ so it'll take a while.)
I'm confused about your first question Crude, do you want the player to be able to fire at anytime or to lock him in? For the locked in, I'd say do it like guitar hero games..the targets have to be hit by a certain space, if they are are you trigger the correct sound or..really, just don't mute the instrument. I thought about using that for my game, instruments on seperate channels that get muted if you got hit. (Thats part of why I want the VST, I figure adding effects would be more interesting.) I haven't tried the seperate channels yet, but I'm concerned about them getting out of sync.
As for being able to fire at any time, the only thing thats coming to mind is to try to create stingers that would play well together and against a simplified backing track. Maybe write a guitar riff, use part of it for the first strike, for each combo after that you let more of the riff play.