If the file names were the same, except for the file extension, it would be pretty easy to write a script to do it. If the file names are NOT the same, except for the extension, it is going to pretty much be impossible, because due to the difference in formats, the contents are going to be wildly different, so you can't compare that.
I'm not sure if by "Also, many of these files either don't have the correct name, or have variations of the name because the sources of the files edited the titles before posting them" you are talking about the book title in the metadata, or the file title or what. A program to search for metadata would have to understand all the formats you are interested in.
I'm not sure if Calibre understands all those formats, but if it does, you can import the books into Calibre, and it will put all the books it thinks are the same, except for format, into the same subdirectory in its library. Don't know if that would be of use to you, or not.
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