Oh no, I am so sorry about what happened to him. At least you know that you did everything you could; I know from experience that rats make awesome pets (much better than most other small furry critters.) At least he is not suffering anymore with that horrible disease; sounds like you did everything you could.
I would possibly have the vet do a postmortem, just to see what had caused all of this.. I wish you my sincere condolences.