Merging Music Libraries, From Different Sources

I have a twist on this, where I'm consolidating a ton of music I've bought over the years, from different sources. That is, the directory structures are not necessarily what iTunes would use, create or expect. Some are just plain-old music files, others are stuffed in mirrored directories, etc.

These consist of *.mp3, *.m4a and some of the old *.m4p files.

Now, I have found a tool (fdupes) that can detect (to some degree) duplicate items, but I am not sure it's using digital signatures to determine content similarity, etc.

My goal is to (finally) unify this monster collection under one directory master tree that I will continue to maintain -- then have iTunes import and use it. Many reasons for doing this, mostly due to iTunes and its rigid controls -- but I do need to keep this unified, so here we go.

I am likely to recursively convert *.mp3 to *.aac prior to any import to iTunes.

In any event, how can I reliably manage this? There are literally thousands of songs, in different directories. Some of these may not have correct metadata, and there's nothing you can do about that but stuff them in one place.

I'm surely not the only person that's run across this difficult scenario. I'd appreciate any pointers!

Thanks.