That sounds really rough.

I think it could be stress related, that's a big thing to happen and sometimes bubs don't cope with changes very well. On the other hand, it could be a food allergy, it's just so hard to tell isn't it? I'd definetly either be going to a different GP for a second opinion, or getting a referal for a paed.

I hope things get better soon, try and rest as much as possible!