Hi K.,
My doctor recommends waiting until the baby is one year old before introducing any dairy, so that is what I did.
I had a similar problem. I thought it would be easy to transition from stinky old formula to sweet, cold cow's milk. Boy was I wrong!! My daughter HATED cow's milk. I tried warming it, serving it cold, in a bottle, a sippy, a regular cup, over cereal, mixed with formula---NOTHING worked. She also got a terrible diaper rash during this time--first one ever. We were convinced that she had a milk allergy, had her tested---NOPE---but she still wouldn't drink milk. She did start liking yogurt and cheese at about 13 months, but still no milk.
Finally, I started putting some sugar or strawberry flavoring in it, and she started drinking it. She was 14 months old before she was totally off formula and on milk. I think she had a milk intolerance, so milk made her feel bad, and she knew it. I think they are made to know when they are ready for milk, so maybe you need to hold off for a couple of weeks and try again. By the way, chocolate flavoring is not recommended, but sugar is okay to start.
I used Enfamil Next Step in place of formula and as a transition into milk. Maybe that would help your son, too. Try yogurt and cheese if okayed by the pediatrician, too.
My baby also cuts WAY back on her milk and food consumption during teething, so for me that is normal. She ususally makes up for it a few days later.
Still, I think I would buy some more formula and ease him into milk. Also, it is the perfect time to get him off the bottle by only serving milk in a cup. My pedi forgot to tell me that, and we got fussed at at her 15 month appt.
Good luck! Hope some of this helps.