Hi, M.. Straight whole milk is very different from formula which is based on milk. Formula has a lot of stuff added, and some formulas have the milk proteins and fats partially broken down so that they are easier to digest. That's why whole milk can give a child a different reaction than forumula.
Try that Good Start stuff (I'm not sure what the name is) or something similar. It's milk for toddlers who are ready to go from bottle to sippy cup. It's easier to digest and has more vitamins than whole milk.
You can also give her soy milk that has been enriched with vitamins and such. Her stool shouldn't be affected badly, but she may have gas from it until she gets used to it.
Any kind of changes to a child's diet are going to produce some changes in digestion and stool.
Don't be afraid to give her natural juices which you know she's not allergic to. Orange juice can sometimes be a problem, so try unsweetened apple juice -- that's good for the digestion and stool, by the way.
I hope everything works out with her transition.
Peace,
Syl