Finally, I solved the problem by myself.
It was a bad idea to build my hexagons first and trying to clone it to a sphere, as it was mathematically impossible to build sphere by hexagons.
So I created a icosahedron type sphere and later on I subdivided the sphere using a hyperNURBS subdivide option. And melted the edges and left over with the sphere with hexagons and some pentagons. Created my mograph clone and created a cylinder and used object to edge and scale to edge. So now I have a fully control of mograph to be animated later on.