I'm so sorry. I wish I could have been on earlier to help, but I don't think anything else could have been done for her.
To determine if this was from tooth root issues, a URI, or myxi, the vet may want to do a necropsy. I also wonder how quickly the disease set on, as it seems that it come upon her very suddenly.
Truffles was a beautiful bunny and I can tell she meant a lot to you. She did have a good long life, and it's possible that she was just hiding a tooth root infection from you for a long time (rabbits are very good at hiding illnesses), until it became more than she could handle, and the infection got into the rest of her system and she couldn't recover from the bacterial toxins taking over her body. I'm so sorry you lost her.