Q&A: baby with compromised immune system

This is going to be more of a reader call, because I'm at a loss. We really need help from anyone with experience with anything like this. Kim writes:

"I'm hoping you can help with an issue with my baby.  He was 11 months old on Friday and has been consistently sick throughout the first year.  Severe colic, acid reflux and after an anaphilactic reaction diagnosed with severe food allergies at 5 months.  Lately (since Christmas) he has been sick almost non-stop with several different things, one was a double ear infection but the others we more confusing.  He has had two viral infections (sores on the throat) and two fevers with vomiting a week apart.  The throat thing he has has about a half a dozen times in six months but twice in the last month.  When he has vomiting by itself we assume it's tied to the allergies but when it is accompanied by a fever it indicates some sort of infection......he has no other symptoms....just fever and vomiting.  We have a three-year-old that hasn't been sick since last summer.

My worry is that his immune system is somehow compromised......maybe because of the allergies.  He is allergic to beef, all dairy, eggs, shellfish, tree nuts, celery, green beans and cantelope (also house dust & dogs).  He has no environmental allergies so spending time outside doesn't seem to effect him at all.  We live in a mild climate (Arizona).

I have tried some natural remedies for the viral stuff but the only thing that seems to give him any relief is Motrin.

He was 9 pounds at birth, breastfed until this past weekend (he weaned on his own) and is 26 pounds now.  He has a very hearty appetite and we buy all his food fresh from the natural food market and blend what he can't eat on his own."

I'm definitely out of my depth with this one.

It doesn't seem to be environmental, since the 3-year-old isn't affected.

It's not a reaction to his diet, since you've diagnosed the food allergies and are eating as clean as possible. And the viral infections wouldn't have anything to do with food allergies.

It sounds to me like you're right, and his immune system is weak. Unfortunately, I don't know exactly what to do to help you improve it. I'd definitely start with probiotics and also cranio-sacral therapy. The probiotics will help him get good flora in his stomach, and the cranio-sacral therapy will help release anything blocking his nerve and lymphatic flow. But after that, I don't have any other suggestions.

Anyone else have any insights into this tough situation?