P.S. Anything naturally I can try to fight this on my own?  I used to take Align regularly but stopped so will pick some up again but think that's more of a preventative thing rather than a treatment

You can't fight it on your own without knowing what you're fighting. This doesn't sound like pouchitis to me, since you haven't described any connection between the pain and pooping.  Lots of us can start antioibiotics without an office visit, but that's usually after we've established a clear pattern that is very likely to be pouchitis again, and reached an understanding with our doctor. 

It gets me up at night a bit more than normal.  In the day I'll go more but that's just because trying to relieve the pain...not an urgency.

Today it's been more burning so maybe it's a gastritis flare up?  In the past with gastritis my symptoms were mainlt nausea which is why I thought pouchitis and not gastritis.

If you've had gastritis before then that would be my first guess. It could also be a peptic ulcer, and there are other possibilities. Perhaps you could place a phone call to your doctor and discuss whether a visit is necessary. If you treat a peptic ulcer as gastritis you might just mask it.