Problem with the original CFJ stages is that they includes characters in the background that weren't originally playable in that game. And since this Mugen game has most of them as playable characters it would be weird seeing them and their NPC selves at the same time lol.
All of the cameos can be easily removed with fighter factory (make sure you remove the shadows from the npcs, if any) plus double check the def file in case of BG errors.
He who is brave is free! - Lucius Annaeus Seneca