A.M.
My son has reflux and this sounded JUST like him! He is going to be 3 in a few weeks and i will say about 6 months ago he really started to eat "normally". We would try and force him to eat but it ended up bad...him screaming, us frusterated. his dr told me that he WILL eat when he is hungry. It was nerve racking for me cause he would go almost 2 days sometimes without eating food...maybe a few bites here or there but no meals. He would drink milk and water/juice but not food. We put him on Zantac and he is eating like crazy...i have to stop him now! It was scary and made me nervous but his weight was always on target and he had energy and was healthy.
One thing that i did in the mornings to get some protein in him was a protein shake... i would blend fruits with milk some ice and protein powder. Sometimes i would add a yogurt instead of protein powder. Maybe try that. He thought it was a treat and LOVED it!
Good luck.