does this sound like allergies/intolerances?

[JoyMC]

i'm sure you guys get this kind of question all the time, but i'd be ever so grateful for some feedback. i love my naturopath, but she seems to have hit a wall. 

my DS is 10 months. from birth (at home), he has been super mister cranky pants. pretty much never happy as a tiny guy. then, around 7 months the whole family had a virus, including DS, and after that his crankiness increased a TON. nights are the WORST. hours of screaming. (with us, not alone.) like, someone is stabbing him in the eye screaming.

i wasn't worried about food allergies because his poop was pretty much normal and he has never had any rashes or weird skin stuff. but we've been through extensive chiropratic and the naturopath can't find anything wrong except very low vitamin D (hello, Seattle). so now i'm taking a new look at food allergies/sensitivities, and in the last couple weeks his poops have gotten kind of weird and grainy. i read that gluten intolerance can be triggered by a virus, so that made me pay a bit more attention.

we breastfeed, no formula, we started solids around the same time that virus hit, and we do BLW. we eat all organic, whole foods, with a traditional foods bent. lots of raw dairy, grass fed meat, fruits and vegetables, whole grains, coconut oil, etc. i take probiotics (Kirkman Labs and homemade kefir) but haven't given them directly to him. 

the naturopath wants us to do a blood test for food allergies, which we have scheduled, but that won't tell us the whole picture, will it? i mean, there are lots of sensitivities that won't show up, right? i am on day five of an elimination diet - not the super strict turkey and pears one, but cutting out all the biggies - wheat, soy, corn, dairy, eggs, tomatoes, citrus, berries, nuts, maybe a couple other things. there's a list on the fridge.  the first couple nights were actually super improved, but then the last couple have been intensely awful. 

so, any thoughts?

oh, and he clutches at his ears constantly, but his ears check out fine. for what that's worth. and blueberries and peas come through his poop completely undigested. (sorry for the random facts; just trying to include all the info.

thanks for any input!!