This is something I'm really interested in, specifically for my music studies. ...
I think almost all the points/functionality you mention there can be delivered using MS OneNote - certainly I already do roughly 80% of what you seem to need.
Like most things, OneNote has its limitations, but they probably don't intrude for the sort of functionality you seem to be describing.
As always, rather than rely on other people's opinions, I'd recommend you "suck it and see".




