I have a 4 year old male Shiba Inu. Up until about the last month, everything was good. For the last month, he started chewing on himself. He had actually chewed through a layer of skin on his tail. We took him to the vet, she couldn't figure out why he was, other than maybe allergy related. (he takes allergy prescription meds already). Finally, I had exhausted myself on the issue, so took him in to get a good grooming, as he has been biting at himself more often. They gave him a good treatment, removed a lot of excess hair, and they said they found one flea on him. He came home yesterday from the doggie salon, and has already chewed a bald spot into his lower back by his tail. Yesterday, after the visit, I let him outside like usual, but just happened to watch him, and he pooped like usual, but this was the first time I saw him turn back around and eat it. I witnessed him doing it again this morning. These are the only times I've seen him eat it, but doesn't mean he hasn't before. We usually let him roam in the backyard until he barks to come inside. He's been eating Blue Buffalo dog food since August. This was recommended by his obedience class instructor. He seems to like it, but didn't know if that would be related or not. Could all of this be related to a food allergy or deficiency? If so, any recommendations on what food we should change to?

Dogs eat their own feces for many different reasons, I don't think anyone could give you a definitive answer on why.
Simple solution is to pick up the poop as soon as the dog goes, but you can also try adding crushed pineapple to his food (if he will eat it) apparently it makes the poo less appealing to them.

Fleas are hard to spot at the best of times, but on a thick coated dog there could have been more than just one on him (I would put money on it) and some dogs can be allergic to fleas which makes the problem worse.

I personally would wait a while until you know all the fleas are gone before changing the food, Blue Buffalo is supposed to be a very good brand.
Once you are sure it isn't a flea allergy you can try changing it.

Seeing as your dog is is showing two signs of allergy related issues, I would suggest a food change. Like Shazzy mentioned, dogs eat their own feces for a few different reasons, one of those reasons is a lack of nutrients in their diet.

You mentioned he is on allergy meds now, have you figured out what was causing his allergies? I am going to take a guess at it being the type of food you are feeding him. A lot of dogs have allergies to wheat and grains, so feeding them commercial brands which are high in fillers such as wheat, grains and corn and other horribly by products, makes them itch like crazy.

Seeing as the groomer did find a flea, it wouldn't hurt to get a treatment from your vet. You can also try adding some omega oils such as a can of sardines, salmon oil or cod liver oil.

What brand of food are you feeding him now?