We use Almond Breeze, although it does have some soy, it isn't primarily soy. I also just posted about the best new rice cream...although it may have some soy, too.
It took my stomach quite a while to heal...I'd definitely say at least months. I took fish oil which is supposed to help heal the gut. I've also heard some people swear by aloe vera juice to help restore a healthy gut.
Hmmm...I just added back a food allergy page in TGF, and I think one of the links on leaky gut mentioned some things that may help. Carol (concerned lady) also had some reflux tips that might be useful. I'll try to be back with some links for things soon.
http://www.mdheal.org/leakygut.htm
and see Appendix B
http://cantbreathesuspectvcd.com/page10.html
I think that it can take a bit longer for the stomach aches to resolve, but you might want to watch the casein, soy, corn for a while.