Need help ladies

So I have always exclusively pumped for my son, I made plenty of milk enough to feed him and freeze some at every session. Then my supply dropped drastically (lots of stress right now) and I noticed that as I supplemented with formula my breast milk started giving him a sprinkled red rash on his face and chest. He was also getting super crabby and staying up crying for three nights in a row. When I noticed the rash I called the pediatrician and she had him come in. I showed her the rash that appeared seconds after starting a breast milk bottle... she was puzzled. She started him on soy formula and had me cut dairy out of my diet. It's been 4 days and he has the smelliest gas and has gone from 10 poopy diapers a day to 1 or 2 and it's runny brown or green foul smelling poo. Also tonight I tried giving him breast milk again and the rash appeared on his chest, but not his face like before. Anyone know anything about this?? Experienced this?? It's like the kid is allergic to my breast milk.