Well the world that gives the highest output of souls is the Shrine of Storms world, especially once you reach 4-2, killing reapers nets you 5K souls, without any soul gain boosting accesories.
Even the skeletons in 4-1 gives you a good amount of souls, 400 to 500 for Silver skeletons, 800 for Golden Skeletons and 1100 for Black Skeletons. Plus if you shoot down mantas, each one gives you close to 1000 souls.
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