Sounds like you got a good plan to improve it! About the skills, I think you could put an item the player can use to read what the skills do. The only problem would be that would cost a turn, but maybe that can be balanced (maybe it also guards? Just an idea that came to mind as typing)? Or maybe an optional 'challenge' the player can enter that is just a room to read up on all of this. Would require the player to remember what they do, but it would be a start.
I think a separate group of short, quick, hard hitting bosses might be fun! I say go for it! That can be say a track B or something, and keep what you have on track A? Though I still think a couple leading up to that boss could be a good idea, as usually making players redo the first real battle on average is a great way to make them quit and not come back these days (or so I've learned). Hence why I suggested a couple easier ones first.
Best of luck as you continue to work on this!