Just watch your knee and be gentle with it. As you progress with the cleansing see if there is any change. In my own experience I just wake up one day and realize that the pain or discomfort has been gone for some time and I didn't notice it go. If it persists, then you can go have someone look at it.
I find Shiatsu is very interesting. Find a book on it and take a look at the meridians. See if there is some logic to the places that you are feeling pain based on what cleansing you are doing, or that needs to be done.