I believe the protocol doesn’t endorse enzymes because they break food down into simple sugars which actually feed the candida. It’s also why products like Candex aren’t recommended.
I experienced a lot of cramps and pains etc. that perhaps were similar to yours. I would usually experience it after taking antifungals. I think it was perhaps a combination of gas and the constipation I had at the time. It was really painful (and I think I might have a hemroid now because of it). Anyway, long story short. A combination of digestive bitters and betaine HCL fixed the situation for me.