Do these replacements work in recipes from other mods?
For example a buildcraft wood gear requires four sticks. Next, a stone gear is four cobblestone around a wood gear.
Could the stone gear be made with Gabbro around a wood gear, or any of the other rocks supported in any combination?
EDIT: I have a suggestion to get vanilla cobblestone - mix one of every type of stone together to get that number of cobblestone blocks. I can't remember how many different types you have but if there are 8 you would put 1 of each in the crafting grid and get 8 pieces of cobble out.
That would encourage proper stone mining as well as for ores
Lava/Water mechanics still work. So just make a cobble gen and you get your vanilla stone.