Well, I didn't know Prevnar had soy protein in it so thanks for sharing. DD had 3 Prevnar shots - at 2,4, and 6 months. She has a pretty significant reaction to soy (the worst of all her reactions). Truthfully, I didn't notice a reaction to the Prevnar shot but at the time I didn't realize she was reacting at all and we had her on Soy formula as a supplement almost every day too.
So, that's probably no help to you at all. But the bottom line is the Prevnar didn't seem to significantly worsen her GI symptoms or cause immediate reactions. We will never know what kind of long term damage was done.