Sounds similar to what Clark had (although it had nothing to do with processing food). He was diagnosed with immune mediated punctate keratitis. The vet used a camera and took a picture of his eye through the scope, Clark's eye looked like a field of stars, so many pin point spots . Long road to recovery, but he is fine now. If you want I still have the report from the opthomologist I can send you a copy.
He was treated with Cyclosporine 0.2% 3.5Gm Ophth Ointment.
Hope your baby is feeling better.