You could try to open the 4000BC autosave (or any other save, tho the later the save, the more stuff you will need to clean out) in WB, save as scenario and look what you can do from there. With some Notepad editing (you can open WBS saves in notepad) it should be possible to keep the map but revert the civs and starting positions to random.
Creation & Customizations forums would be a place to ask for more detail.
If you start the game as a custom game, then open the worldbuilder on the first turn and save it as a scenario, you should be able to call it up as a scenario and change which civ you are playing, as well as the custom settings, I think.
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