It’s hard to get specific w/out professional guidance and some diagnostics.
A couple of things we’ve used for gut issues:

A general anti-viral/bacterial/fungal like lauricidin / monolaurin
http://www.lauricidin.com/
http://www.heranswer.com/monolaurin.asp

A general gut soother like Mucosagen
http://www.optimalhealthnetwork.com/product.asp?specific=jnnmmpe0

If you think it is a digestion issue (and anyway because this is AMAZING for CF and all of us) - read ‘Micromiracles – the healing power of enzymes’ by Ellen Culter
Did you know that there is a period of 1 hour that food sits before it gets digested by the stomach. Ideally it is a time of pre-digestion. Then pre-digested food goes to the stomach – then GI. The pancreas is signaled to release enzymes according to the level of pre-digestion. With no pre-digestion the pancreas has to work extra hard. And an extra hard working Pancreas leads to an enlarged pancreas, etc. CF enzymes are animal based and are designed to work in the GI. Since natural enzymes are destroyed in cooking – the pre-digested stage is completely wasted. ( Quite important to know especially with CF!!!! I am amazed that pre-digestion enzymes are not a rule with CF!...I never knew any of this...)

Anyway, pre-digestion stage enzymes are vegetarian, safe and easy to use. Maybe try to help the digestion by trying one after doing your own research? I am amazed at the improved overall health I have seen in my child…and me.

The book explains why to take enzymes between meals too. (We are doing both.)

Anyway here is an example of enzyme choices. Also check out Serratiopeptidase & Virastop & MucoStop for CF at Enzymedica. (Mucostop has been a Dream for me with the Winter cold season.)(& You can find them cheaper on the internet...)

http://www.enzymesinc.com/wellzymes/wellzymes.html

http://www.enzymedica.com/