//Draw cubes and store data
function Awake () {
for(var z=0;z<8;z++)
{
    for(var y=0;y<8;y++)
    {
       for(var x=0;x<8;x++)
       {

         Instantiate(newCube,position,rotation);
         newCube.position = position;
         cubeList[cubeCount].Cube = newCube;

         cubeCount++;
         position.x += 1.1;
       }
       position.x = 0;
       position.y += 1.1;
    }
    position.y = 0;
    position.z += 1.1;
}
}
At the moment to find the cube in the array I am using:

function OnMouseDown()
{

for(i=0;i<511;i++)
{

    if(transform.position.x == Main.cubeList[i].xpos)
    {
       Main.cubeList[i].colour = currentColour;
                Main.cubeList[i].selected = isSelected;

    }
}
}