I'm afraid I can't help much regarding Kefir.
However step one definitely is treating the leaky gut. AND.... reestablishing mineral equilibrium. When you say you are experiencing muscle spasms/pain, you are saying your minerals are out of balance. Candida depletes magnesium and it is quite standard to have to compensate for its deficiency, when your metabolism is in lack of mag. it goes into your muscle to retrieve some, which causes muscle spasms/pain. Muscle spasms/pain may be caused by quite a few mineral deficiency, magnesium generally is the culprit when candida is concerned, calcium could also be an issue. (Zinc deficiency will otherwise manifest itself through itchy rashes.)
It is likey that the mag. deficiency is simply due to intestinal malabsorption, due to leaky gut/inflammation. The first step is to get rid of the intestinal inflammation/pain
1- with the diet (to prevent it)
2- with marshmallow root tea (boil it 15 minutes it is a root) when in pain
Once the leaky gut is healed and the minerals balanced, then it is important to add friendly bacteria (I like home-made sauerkraut best).