1. These are Persistence Points, to be used during the One Life event and are used to improve bonuses in this mode.
2. I think you got it. The bonuses displayed are the active bonuses, if you refine your ring then the bonuses are replaced by other bonuses, unless you have blocked a line by clicking on it (but then it will cost more in ore).
3. Nop! it just allows you to have more lines.
I hope it's clearer for you now. Thank you very much for your feedback, it helps me (and it makes me happy)!