mcd

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?

Have you tried to deactivate the percentlevel password? Maybe the game considers it still an opponents mon

What was your solution? So that anyone that has the same problem in the future can know

That's the wrong spot, you are supposed to interact with it in the upper right corner of the map. Get it to move up there, then talk to it

When did you last save?

Currently, only Aura break is available, as not all Zygarde cells can be found yet, only like 130 out of 150

You need to run the updater in the files

Only way I can think of is using debug mode to teleport to the cave, I don't think there is an alternative way

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