Sorry for the late response, but somehow this topic got buried.
I started on low dose MTX pills almost 30 years ago. It was a slow process - something like 1 pill one week, 2 the next....... How much have you been prescribed? What about folic acid - were you prescribed this? Presumably you're taking the pills rather than the injection.
I've never experienced stomach or esophagus pain - actually, I've never heard of anyone who had this from taking MTX.
Are you sure there isn't something else going on?