sounds like you have one hell of a mess on your hands. No pun intended.
Yeah, uneven floors can cause issues with leakage on toilets. You need to level that floor out somehow under there. Then, reinstall the plumbing as it's supposed to be - no double flanges with multiple wax rings. The more junk you put under there the more potential leak points you develop.
And if all that doesn't work, it's time for a new toilet.
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