Will apple cider vinegar make the stomach acid or alkaline?

Acid, it is acetic acid.

I have a really bad problem with candida. So bad that most probiotics shut down my digestive system. I can eat yogurt, but kefir and most probiotic supplements sheut down my digestion.

The probiotics should not cause this. The flora generate serotonin that regulate bowel movements. Are you sure it is not something else such as a lactose intolerance? Commercial yogurts are fermented longer than commercial kefirs resulting in little if any lactose. Have you tried making kefir with water or coconut milk?

Can anyone tell me where to find FOS and how to use it?

Check with your local health food store. If they don't carry it then they should be able to order it for you or you can find it online.

http://www.herbs-wholesale.com/keywords/FOS.html