A note about WIC (I worked for them). WIC is NOT required to give the formula a client "needs". Formula is just as expensive for the government as it is for families. The formula requirements are different depending on the state and most states are getting more strict with what they will provide. Being that she gets Good Start, I assume she lives in Wisconsin and I don't know that they would give her Similac even with a doctor's note.
I would just try doing 3/4 Similac to 1/4 Good Start and gradually increase the amount of Good Start. Overall the formulas are pretty much the same. It is normal to have digestive problems (spitting up, diarrhea, constipation) when switching formulas. As she gets older she should be able to adjust.
She could talk to her WIC agency about trying a different kind of Good Start such as lactose free or soy. Even though the baby's not lactose intolerant or allergic to milk, he be able to tolerate it better.