T.,
I have two suggestions for you. First, I would call the doctor with questions--they are usually happy to answer questions, and it saves you a co-pay as well as having to drag two kiddos into the doctor. And then, you do have a 9 month check up coming up soon--and the doc could do an exam then, if he didn't feel one was necessary right away.
Second, I have had my daughter on a probiotic since she was born. I think it really helps with intestinal issues. I give her one made by Jarrow that is specifically for infants and young children. You can get it at Vitamin Cottage/Whole Foods etc... I would start mixing a little bit of that in with her foods--the ones that she eats well--and then start adding foods after a few days with the probiotics. They put good bacteria into her intestine, and help her digestive system to function as well as possible. I would add them to your son's foods as well.
Also a great food that is tolerated pretty well by most babies is avocado and bananas. Just take a ripe avocado, mash a little up, and feed it to her. Do the same with banana. Avocado was the only food my daughter ate besides breast milk until she was almost 8 months.
Good luck!