I had to reply to this one because I was 11 years old when I was diagnosed too!
The hardest thing for me about having a late diagnosis was the emotional side of it. But it sounds like your son has been in the hospital and has some experience at least with the medical universe. Even though he was treated for the absolute WRONG thing, he at least knows what it's like to be in the hospital. For me, it was all new and scary.
I always had a cough as a child, but almost my entire family thought I was faking - my uncle accused me of faking to get attention!! My mother was the only one who was persistent and when we finally got the CF diagnosis, boy did everyone else feel like idiots!
Anyway, I was really non-compliant for a long time because I was diagnosed so late in life and I was in major denial. My mother was not strict with me - she believed in letting her kids make and learn from their own mistakes. Of course I love my mother dearly, but she was wrong. My advice to you as a parent is don't ever let your kids get away with wussing out on their treatments, meds, etc.
When I was diagnosed, I had "mild" CF (which was used as the excuse for why nobody caught it sooner - it was just ssooo mild, which I think is BS by the way). Now, at 29 years old, I have severe lung disease and I attribute that almost entirely to my non-compliance and the fact that I wasn't FORCED to do everything I should have been doing to stay healthy as a child. Don't get me wrong, I don't blame anybody for the choices I made. But parents have a responsibility to look out for their kids when their kids make stupid choices, lol!!
So that's my advice - definitely be proactive with the docs and trust your instincts. If you think he needs a tune-up, you're probably right (and you'll get more and more confident about this as time goes on). And never let either of your children slack on treatments - it's harsh, I know - but they will understand once they are old enough to look back on it from a different, adult perspective.
Also, know that even with total 100% compliance, eventually lung function will decrease, that's just the nature of CF (that's my little disclaimer so nobody yells at me for making it sound like your lungs will be perfect forever if you just do your treatments <img src="i/expressions/face-icon-small-tongue.gif" border="0">).