Just because he hasn't had a recent problem with chest/lung infection does not rule out the possibility of CF. I don't understand why your doctor seems to think CF symptoms are only in the lungs.
From what you have posted in the past I still think it is very important that you continue to push for more CF testing to rule out CF -- not just be told "I don't think so" by a doctor -- they need to prove it to you -- it's a dangerous game for them to be playing and it is you and your son who will loose out, not the doctor. CF needs to be treated as CF, your child's health will most likely improve if you could get him the correct diagnosis and treatment.
As for the fishy smell - I'm not sure. My only thoughts are - I know there is some sort of bacteria that women can get (like a yeast infection - in the vagina) which can produce that type of a smell. I suppose it might be possible that a person have that same bacteria in his throat or lungs too??? Purely speculation about that. Also some people have commented that when they are culturing the pseudomonus bacteria in their lungs, there spouse has commented they "have that smell" about them -- don't know if they described it as a fishy smell though.
Regardless of all my guesses -- I really think you should take him in about the smell -- seem like it has to be a bacteria thing somehow .... but also see if you can make any headway into getting more CF testing done -- the GI symptoms and past lung issues really sounds like he could have CF.
Did you notice on one of your previous posts, another woman from Australia posted a phone number for you to call? I think it might have been a CF center --- sure seems like your doctor is not steering you in the right direction yet.