It doesn't matter who he studied under if he is ignoring a positive C-diff test!! I would suggest that you stop the abx until you talk with him at least. Margaret (Teragram) has had C-diff and has found that she can't really use any abx, so do be careful!! With that said, Flagyl is one of the abx used for C-diff infections, and one that is used for these infections
And that " hit it hard and my case was so complex, it wouldn't be helped unless it got hit hard." is baloney. There are plenty of people here, including myself, that have had complex cases and never hit it so hard as to ignore warning signs!
I would also look into seeing another LLMD if this one doesn't understand C-diff well enough to stop the heavy abx when you have a positive test! You surely have enough to cope with without ignoring something as potentially serious as this is.
patient.info/health/clostridium-difficile-leaflet