It's odd that the pouch looks good on a scope and makes me wonder whether some or alL of your issues are from the antibiotics. I would stop the antibiotics, take Pepto Bismol for the gas and bloating and incontinence for a few days and see what happens. If your problem was dietary you would not have had 2 blissful years with the ileostomy, so it makes no sense to me why your GI gave up and sent you to a dietician when based on your history the problems are clearly related to either the J Pouch or the drugs being used to treat it.
You ultimately may decide you want to go to a permanent ileostomy which would be another surgery, but before you do that you might want to go off antibiotics, try PB for a few days and see what happens. PB will knock out the gas, and bloating and maybe the incontinence at night; removal of the antibiotics may release the tailbone and hip pain as it could be side effects of these meds.