Basically you want something that will hash the file contents and compare hashes, this gets around filename differences.
Define where your "final" location will be and compare each drive to that (the 1st one will be the starting point, so pick the best , largest drive
fdupes / rmlint will get you most of the way there.
Then you'll want to compare similar files, so maybe something like meld or beyondcompare might help.
This will take a loooong time, but will be worth it