in colour calibration stage I would not worry about delays. because you simply put colour in front of rectangle. after that you can close window.
if you using kinect for head and body calibration then you actually do’t need calibrate… because it is same tracking system. i know it is far from perfect now from user interface communication.
Regarding led tracking quality, can you tell where problem is as not clear for me.
Also please let me know which versino of Kinect do you have?