Diflucan can cause liver problems so it is important to do liver function tests regularly while on it. Imo diflucan should only be used as a last resort.
" I am going to try and cut that down to every other day. Maybe part of the problem is that I don't have enough stomach acid? "
Bingo. Reflux is linked with low stoch acid. Cayenne will help increase stomach acid. If that doesn't help enough, you could try Wormwood . Be careful with Wormwood though. Don't use too much, and don't take it for more than a month(then at least 3 months off).