Couple quick questions:
how much formula is he receiving daily?
how many solid feedings / day?
What you are experiencing is a nursing strike.
I think that inadvertently, in trying to solve a "problem" which wasn't really a problem, your doctor may have caused an actual problem.
It is very common, looking at the typical growth charts (based to a large extent on FF babies) for BF babies to look "skinny."
Oh, I'm so glad to hear that things are going better!