As you noticed, I had to temporarily enable DDoS protection. Someone is trying quite effectively to distract me from my activities ;p Unfortunately, this may cause some issues with the federation. I will try to cut off the traffic as soon as possible and return to normal operation. Thank you for all your support and patience! :)
Thanks for keep things running well. Is the DDOS mitigation confirmed to be causing federation issues or is it speculation at this point? How does Mastodon deal with it?
Edit: Are you able to create a rule to bypass the check for logged in users?