Most people on the Candida Forum , including myself, highly recommend using apple cider vinegar to treat candida overgrowth. If you are seeing mucous in your stool, that could be candida coming at as it is being killed by the ACV. I know I have got out a lot of candida using ACV, especially ACV enemas (you really have to be careful with these though).
I'm sure that some people may have a bad reaction to ACV so if you really feel like its harming you, then you should probably stop taking it, but just keep in mind if you do have a candida overgrowth problem, its not going to feel good when you start killing it (this is called die-off or the herxheimer reaction).