80% of our immune system is in the gut, so I would definitely recommend looking at a probiotic. Yakult etc are no good, inner health is ok but if you want a really good go for something like bioceuticals - I get ours from the health food shop. From what you're saying, cutting out dairy to see if it helps sounds like a good idea. You will need to eliminate it completely for at least 2 weeks, then slowly reintroduce and look for signs that it's effecting him (energy levels, sleep patterns etc as well as the more obvious ones.) We recently eliminated wheat too as dairy helped, but not enough.
It may also be worth visiting a chiro or osteo so that they can make sure his body is working at the optimum level to be fighting things off effectively.
Good luck, we are going through the same thing with my DD at the moment and it's no fun. I must say though, I was worried about the elimination diet but actually it's been fine, just a bit expensive, but there are plenty of options available these days.
Without alarming anyone, but wanting to ensure all the boxes are ticked, it is worth noting that repeated chest infections can also be a sign of other problems, such as Cystic Fibrosis. Even though the heel ***** test may have returned an all clear for CF, it is important to understand that it only tests for the 40 most common varitations whereas there are over 1400 known. If in doubt, insist your Doctor have your child tested again.
Interesting fact: before testing for CF was invented, midwives would lick a babies skin after birth. If it was salty, the midwife would hand the baby to the mother and tell her to go home and love it because it would pass away soon. Thank god for modern medicine, people with CF can now live a long healthy life.
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