Parenting: 3-6-Month-Olds Community

As posted on Baby's First Year Board:
Our 3 month old son has had a stuffy nose for 9 or 10 weeks now. It started when he was about 2 weeks old. At his 4 week appointment the pedi told us to use the saline drops, suction it out and use a cool mist humidifier. We've been doing so ever since-except we use the saline mist b/c he doesn't like drops very well. It was still present so we took him back at 6 weeks. The pedi did a nose culture and ordered labs and discovered he had MRSA-a staph infection in the nose. After 10 days of heavy anitbiotics and 5 days of nose drops the staph went away but the nose congestion didn't. I took him back at 8 weeks-pedi said same thing. Took him back at 10 weeks-same thing. Called again-pedi said to try a nose aspirator that can suction better than the bulb suction and continue saline drops and humidifier and if he's not better in a couple of days he wants to see him again. Not only does he have the nose congestion but I believe he also has drainage in his throat which he gets choked on and coughs because of it. He's starting to get choked on the drainage and spit up quite often. We keep him elevated at feedings, when he's playing and when he's asleep. The nose congestion isn't getting any better and he's still getting choked on his spit/drainage a lot. We believe he's also beginning to teeth so that's more saliva he's getting choked on. The good in all of this is that he's demeanor is still good, no temp. and no change in feedings.

My question is-have we missed anything/does any one know of anything that might help?? I'm so ready for my little guy to be over this. Thanks.