Well, I can only imagine what the poor little fellow was into in the last year...probably all sorts of stinky stuff.
If he is cleared at the vet of all the medical possibilities (yeast, anal glands, etc.), then I would treat it as if it were an external issue...maybe a few more baths are in order? What do people usually do for a skunk? Does tomato juice really work? Maybe you can ask your vet for any ideas on how to deodorize him.
Thanks for keeping us updated. I think we have all fallen in love with this miracle pup!!!!