I'm sad to say that it could take years for your digestive tract to fully heal. Mine is slowly healing but it's been many years since I've started trying to heal from candida. It's such a painstakingly slow process.
You could be suffering die off whihc means your elimination organs are overloaded. Be very careful and baby your liver ( especially taking these strong meds ). I've found liver to be key in all this...and it can take years to strengthen this organ ( as has been my case ). No use trying to kill anything when your liver is too weak to expel the waste.