Minecraft convert block to entity form
Solution 1:
Honestly, if you are using build craft, don't bother with a cobblestone factory, just work toward a building a quarry and you will have all the cobblestone you could ever want.
When I make my quarries, I usually filter out the cobblestone and feed it in to a chain of 6 double chests and then feed the overflow in to IC's recyclers.
Solution 2:
You can use an automated miner.
You make a cobblestone generator that using pistons to push the cobblestone into the area that the autominer mines.
Solution 3:
I don't know about the mods you're using, but the piston mod that was popular before official pistons had the property that two pistons pushing a block at the same time would convert it to a resource entity; there are YouTube videos of cobblestone generators using this feature.