While the lemon does have some cleansing and alkilinizing effects it is not what makes the MC work is mojo. It is just an alkilizing agent and "aid" in the detox processwhile the system is in fasting mode. It is highly unlikely that drinking lemon water 2 or 3 times a day will cause on it's own enough detox to the point that you would readily notice or feel the effects.
It is more likely that your pains are more a coincidence or an effect of the totality of any changes you have made recently to diet and lifestyle.There is no "magic" in the "lemon water" and it does not relate to how the MC works as a whole. The bulk of the effects of the MC is from the fasting aspect "aided' by the nutritional/alkilinizing and other "support" provided by the lemon, cayenne and the simple sugar/carbs from the Maple syrup.