For depth projects, the color of depth cloud and the body is defined by distance from currently selected camera. Actually, we consider that similar colors help to align the body with the point cloud. Thanks you sharing your different opinion though, we'll consider an option for contrast colors.
Yes, currently IK supports only dragging by limb endings. Actually the rotate tool allows more precise positioning and even may seem easier to use than IK when you get used to it.
Currently our animation editor only supports basic functions. And pinning joints is not included. You can apply such corrections in your animation program of choice after exporting from Mocap Studio.
Manual cleanup tools are described in our docs
http://docs.ipisoft.com/Manual_Clean-upSorry, cannot point you to any video tutorial on the topic. We know this is the thing anticipated by many users but were not able to produce them yet.