Just did some quick Yahoo research on puppy strangles and read several articles all of which were fairly consistent to the info in this link:
VETBLOG: Puppy strangles. The orange spots on his nose may be suspect because this disease seems to affect (or is that effect) primarily the face.
I checked up on it to see if puppy strangles was similar to strangles in horses, and as it turns out it isn't.
Have you treated him with a topical antifungal?
I have used hibiclens as a pre-surgery body wash and also to clean the surface wounds where the rods were screwed into my leg.