I'm not sure why you're running into the mouse issues with both games, I'm sure it worked before. But ah well :(
As for tracking combat being harder, I imagine it's just because there are more stats impacting combat this time but I didn't implement a proper pre-battle overview for how it plays out, so I'll try to add that if I make another game like this.
The story goes away when you click so probably is just poor luck that you clicked away just at the wrong time, I'll try adding a delay next time. Luckily though, the story of this game is very minimal to begin with :)
Sadly I don't use github, but I don't expect my code would be much help (it is very messy and uncommented)