I checked the bmx file you made available at soundcloud (sorry, i hadn't taken a look at it before) and yes, this is what I meant. Moving the cutoff like you are already doing with the PeerCtrl machine. Sorry I missed that.
However, since you are using FSMInfector to synthesize, you could try controlling its own cutoff instead of adding that extra Green Filter for example. I usually try to use the least number of machines possible if they get the job done.
Also, for some dynamics, add a cheapo amp to control master volume for the infector and make a real fade in effect along with the cutoff; it sounds good too for intros and bridge passages.
I noticed you are taking the output from infector, splitting it to a green filter and a combo and then inputting these three back to the master. Is this necessary? I always try to stick to a single chain of effects between the generator and the master instead of doing this kind of parallel processing. For me a single chain usually makes things easier when it comes to controlling the amount of effect being applied to a signal source. Of course, it is nice to be able to process one signal in different paths at the same time, but I reckon a simple cascade of effects is generally easier to control. Also, I was thinking to myself here that you COULD end up eating up a lot of bandwidth with just one instrument this way, because of the several harmonics being produced in the side paths (e.g. the combo and the green filter) that could be passing unnoticed. Moreover, parallel processing directly to the master is usually not a good idea, since you have to mute several paths in order to get a single instrument muted when mixing for example.
Just thoughts and personal views, pal. Hope you find them helpful. I am learning here too.
I checked your other audio files at soundcloud. Very good. Keep buzzing!
Cheers!