It is normal to feel the effect of Ki working on you when you are getting used to higher levels. It is normal. It does not mean you have too much Ki, but rather that your are not used to such a level of Ki. There is never excess Ki, but more Ki than you are used to will eventually work on your energy channels to unblock them, thus the hassle in the legs, the nodged, the goose bumps,... the not-wanting-to-remain-still.
Be patient, all will set back into place. When you experience disturbance from your physical body, get up, strech, and get back to your meditation.
We do all kind of things to elevate our energy, but our human ego reacts to this energy by giving us all these reactions, and sucessfuly convincing us that we have "too much ki". Having much Ki has never been a problem, but a blessing. you only have to get used to it before you can even enhance more. Do not let your fear win on this.