Problems with Orion quest

Ever since I beat Taen in the first part of the Orion quest, I have been unable to heal at Pokemon centers. I have also been unable to enter Shade Forest from the starter town, because when I try to enter it tells me that I can’t go in without a pokemon. When I enter from the other side it works fine, but when I get down to the first entrance, I’m blocked by the tree stumps that were present at the start of the game. Lastly, Orion doesn’t appear in the Utira Library so that I can finish the quest. Is there something I can do to fix this?

I don’t think this is related to this problem, but I also have this thing where whenever I start a Battle Pyramid thing, I’m trapped in place, unable to move, without the partner that I was assigned, and have my pokemon at their normal levels.