No problem, I'm glad to help.
So just so I'm clear in my understanding...as long as you're not triggering an audio sample using Mainstage Playback plug-in (because there may be timing issues there), but you're using a software instrument based on sampled instruments as a plug-in to Mainstage, then yes, you can do it in the way I described (and possibly other ways). Essentially, you would create a patch with multiple channel strips. Each of those channel strips would contain the instrument plug-in, plus any effects, that you might need. You then use a combination of what I outlined before to send the right combination to the out and you should be good to go.
The way to test it is to use Logic's own instruments and create a variety of situations which would reflect your needs. Or if you already have the plug-in's you're talking about, then try those. When you get down to the details of the testing I can help you out more by describing in more detail if you like.
Again though, my advice would be to really think about what changes you want "within seconds" i.e. a patch change will work well for that (the technique of assigning specific PC's to direct you to a patch), versus "split second changes" where you should use the Send/Mute technique WITHIN a patch. You just need to think about what you want, when you want it, and plan accordingly.
No VST, Logic wants AU...technically speaking, you might be able to use a VST wrapper but (and I can only speak for myself) I would avoid that.
Sounds like a fun project..good luck!
J.