Soy milk allergy appears after months of soy formula?

I have a soon to be 1 yr old that has been on soy formula since he was three months old because he has a severe milk allergy (it touches his skin and he brakes out in hives). Last week I tried some organic soy milk in his formula, and ever since he has had a horrible rash with horrible diarrhea. I took him to the doctor who didn't listen to me at all and completely ignored the fact that my son was having trouble with something (we are switching and going to an allergist next week). I kept him off anything that had a trace of soy in it, and now he is back to normal. Since he was on soy formula stage 2 without problems does anyone know if it would be safe for him to return to it? I know he needs that nutrition, but I don't know what else to give him unless I put him back on infant formula that is hypoallergenic. He's been drinking pedialyte because of the diarrhea but he can't drink that forever. Any thoughts are welcome, thank you!