After reading your code properly, I think this is the slow part:
for i in circleList:
cylinder = e.extrude(i,100, "box")
What is it that you try to achieve axactly?
It seems that you want a cube of circle growing more and more right?
If this is the case, what you can do is start with the shape you want. And instead of extruding it at every frame, you can just translate the back part of the shape.