You also need to unlock the beacons I think, to do that have a dragon type at the front of the party then interact with two beacons, and a water type for the third one. That should unlock a final crystal near the start of the sanctuary for a total of 8 crystals
The first one is normal, I think it's meant to show the game is not finished just yet. The second one is for the actual progression you have yet to do, once you are done with the content thats left, it should dissapear
you could mine rocks, it might take some time but with saving and reloading you should get one eventually
Alternativley, you can do Dragonites Mail quest which gives a shiny stone as a reward
If you want to do a nuzlocke of Reborn, then yes, turn it off. Reborn is already extremly difficult to nuzlock, you shouldn't make the info available to you unreliable
Pretty sure the quest givers dissapear once you do their legendary quest, to help you keep track which ones you did and which ones you have yet to complete
The Rift should be north from the start of the route, near a rock climb spot. You'll need to use cut to get there. Are you sure you did not just miss it?
Saving her seems to be the best choice, considering you have to go out of your way for that to even be an option. The game's not finished yet, so who knows what that decision means for later on, but yeah, it's probably needed for the best ending