Well then you're missing something. Do you get a lot of Gas.. are you digesting your food properly?(Food combining) Missing enzymes. Not getting enough Zinc is probably a very likely culprit. Taking Omega 3's is good, I'd also take Probiotics it seems like you might be deficient in the probiotic department especially if you're not eating a variety of fermented foods(tempeh, aged cheese, kombucha, kefir, sauerkraut), I'd also look into taking COQ10 but make sure it's efficient with it's bioavailability some research will get you a good answer to that. I'm willing to bet if you're getting sick you're not eating healthy you're just not eating processed foods. It happens with a lot of people figuring out this whole health thing. My roommate eats 'healthy' at least according to your terms but he managed to get sick for two weeks straight while I was sick for maybe a day or two max with the same cold.
I'd start recording meals and your reactions daily to them try out food combining it's hard but it gets easier. That's my two cents, and this is only my opinion based on my own experience.. but I hope something in there helps ya!! Best of luck!