This could get very complicated very quickly

Why not try starting off with a block diagram of all the elements in your system, and the audio/control signal flow between them, then flesh that out into schematics for each element, building and testing each one separately to see how things work.
If you want nice filters, you're probably going to have to actually build those rather than doing it in software. Maybe some of the more senior coders here with vastly more talent than I have will disagree, but I can't see that working out too well in software on an Uno.