Here is the dilemma...if you were having major spit up problems, she may have sensitivity or delayed allergy to casein (milk). I found out about this too late, and it caused some major problems with my son.
Since you see improvements on soy, this may be the case. Now as for the bowl issues...This also leads me to believe she may be having issues with casein...for that is exactly what can happen when your body is trying to get rid of the product that the body does not like.
To avoid the whole issue, you may want to contact a breast milk bank and go that route.
My advise is to get her tested for both HGg and HGe allergies...or tell your ped you want testing done for sensitivities...This saved my child's life...
As for soy in general, yes, it is a hormone based bean, and can cause issues in the future--but is shown to mostly effect boys more than gyrls....I have not found any empirical studies done on soy on infant gyrls....but I do know it had been linked to early puberty and early menstrual cycles.
I have to say that my opinion on the lesser of two evils is using soy if you are noticing an improvement with spitting up (and behaviors)...because an unknown sensitivity or delayed allergy can have worse consequences than the soy bean.
I hope this helped some, and remember--only YOU can make the best decision for your child..YOU are the parent and yes, you have the ultimate say!