If you’ve indeed tried everything, I don’t think there’s anything more anyone can suggest. It covers the most basic step, that is re-issuing an access token to delete the entire website and reconnect it to GitHub. One of that has to work as said by everyone there.
Would you be willing to retry all of them one by one?
There’s yet another comment on there for organization repos: Git Gateway + private repo · Issue #971 · netlify/netlify-cms · GitHub