Hmmmm...not sure ow to tell if it's teeth or not. When we started my dd on cow's milk, we did what you are doing, and made the switch very gradually, 1/2 ounce at a time. We'd wait about 10 days before adding more.
How long did you wait before adding more milk? When you began, you did 2 oz milk to 4 oz nutramigen...how long did you stay at that ratio and look for signs? When you went to 3:3, did the fussiness start right away?? Like the same day?
If he was ok with 2 oz milk and 4 oz formula, then maybe go back to that ratio until the teething is past?? If he still fusses at that ratio and he didn't fuss before, then we could bet it's teeth, right??