Liz- I have used amoxicillin and it was effective in treating my pouchitis, but being a man, I have never been pregnant or used it when pregnant. Although my prior thoughts on the subject were shot down, it is or should be common sense that an antibiotic that is not systemically absorbed (xifaxin) is likely to be less risky, if not risk free, than an antibiotic that is absorbed systemically (flagyl and amoxicillin).
That being said, and apparently I have to add this caveat to my posts here although it should also be obvious or common sense, any suggestion I post here is for the express purpose of giving you ideas to discuss with your doctor and not to act upon on your own. Obviously, these antibiotics cannot be obtained without a scrip from your doctor, anyway. This caveat of running my suggestions by your doctor shall apply to any post I make on any suggestion I make on this board. All posters here are anonymous and we do not know their medical histories as do their doctors.
Good luck with resolving this tricky issue. From your last post it sounds like your pouchitis is similar to mine when not treated.