It sounds to me like a specific barium swallow needs to be done to see why he doesn't want to swallow. If he has breathing problems, I could recommend our doctor at National Jewish and she'd get order one right away. Usually the next day or two.
Also, we have a great feeding therapist that specializes in the little guys. Our son was 11 mos when he first saw her. One of her recommendations was pirates booty (Cheetos without the mess) and the puffs in the toddler aisle. Something else she told us to get that worked wonders was the pre-toothbrushes. Nuby makes some with a nice handle to hold. Our son loved them. They are very theraputic for feeling the mouth, so most kids hate them. Also, when you brush his teeth, brush the insides of his cheeks, the roof of his mouth and his tongue. I know there were other things, but that's all that comes to mind right away.
The sooner you get help for him, the less therapy you'll need later. Most kids who need feeding therapy also need speech therapy. With the help we got, our son has barely qualified for speech therapy. I wonder if we got gotten more help sooner, if he would need it at all. Getting speech therapy is not nearly as easy as the feeding therapy.
I don't mean to scare you, but it sounds like your doctor was like ours. It wasn't so much that he didn't know enough, as that he wasn't familiar with these type of issues. I actually have heard from others that is not too uncommon. Let me know if you want names and numbers.