I would go ahead and make an appointment with another pedi, or, just go ahead and go to the ER at the Children's hospital. I almost lost my oldest at 8 months, turns out she had pneumococcus. The doctor's would not listen to me, but, I knew something was wrong. I went from doctor to doctor for weeks, maybe months. It was underlying, and, by the time we got her to the hospital, it was almost to her brain, she had 105 temp, and, she was so lethargic that she could not move. It took them almost an hour to get an IV in, and, she almost died. (much of this, I learned after the fact.)
We learned a lot during her week long stay in the hospital pumping antibiotics the entire time. She got better, and, relapsed a week later. At that point, we were running more tests in the ER. Turns out, her (and I), are immune to immunizations. Meaning, they do not work on us. So, she was exposed to something, and, it started out as just what seemed like a simple cold to the docs, (most likely, not enough of an exposure to put her down for the count, but, enough that she could not fight it on her own. I was breastfeeding, which probably helped, but, stopped about the time she got really, really bad.). My mothers' instincts kept telling me something was not right. (horrible cough at night that would not go away.) Something else, she had this smell. It was almost like a smell that only I could smell. I guess it was nature's way of saying, "hey mom, fix this kid!" The smell would not go away. I smelled it on her the whole time, until she was finally better. I've had 2 more kids, and, never experienced anything like that again. It wasn't like it was a dirty smell, it really was like nature was alarming me to fix her.
Anyway, my point is, fix him momma. Get another opinion ASAP. You know best, your instinct is saying something is wrong, you have concerns. Get him somewhere NOW, and, insist they run every test if you have to, (or, have someone look at what was already taken so he doesn't have to be poked anymore, although, babies seem to take it really easy), until they can figure out what is wrong.
I hope he gets better. Keep us updated. :)