Hi, I'm trying to make a new biome, but I don't want it to have stone underneath, but one of my custom blocks. I already know how to replace the "filler" block and the "top" blocks, but neither of these affect the stone. I'd also like this to not cause a lot of lag when generating.

Well, then is there any way I could generate OVER the stone to make it into something else?

Theoretically you could create a biome decorator (similar to one that you might create for a custom tree or structure, or a custom ore) that simply grabs all the stone and changes it to your custom block type. I don't know how the default biome decorators would deal with that, but you might have to overwrite the dirt, gravel, and vanilla ores too (unless you want those). I also have no idea how expensive that would be in terms of chunk decoration time. Without doing wild hacks to the default ChunkProviders, a decorator will probably be your best shot.

Best way to do this is in the replaceblocksforbiome in ChunkProviderGenerate.  Trying to replace/place a crap load of blocks (like every stone block for example) in the biome decorator would just cause a lot of lag from what I've seen.

Is there a way to do this without editing base classes?!

Anyone have an answer? Even if I could use the decorator to replace it all at this point.

Build a new world generator, with a new dimension.

You can overwrite the default World Type, and when you do so you can specify a new WorldType class, in that custom worldtype class you can then assign a custom chunkprovidergenerate.