Both nutramigen and alimentum are corn based with trace amounts of dairy proteins. He could be reacting to either of those things.
You should probably switch him to an amino-based formula, such as Neocate or Elacare. They are by rx only and are not always covered by insurance. They are VERY expensive but if your LO is reacting to "safe" formulas those might be your only choice.
Have you seen a pediatric GI. They are the ones who diagnosed my LO with MSPI and who would have written the script for Neocate if it was needed.