My photo library now a complete mess... help needed!

Oh woe is me!
I decided to use a referenced library, and used A3 to move all my gathered photos into a Master Library on another drive.
First thing that went wrong.... A3 can't tell the difference between JPG and jpg, so I ended up with piles of duplicates in the projects.
Second thing (which I don't think is an A3 problem, but nobody has offered any help over at the MacOs threads) is that instead of giving a warning message that a file already exists, the files are simply being copied with a numerical addition, e.g. D2X_77777-(2).
So I not only have piles of duplicates in A3, I have piles in the Master Library too!
And just to add to my troubles, a lot of pictures are suddenly "broken" to the source.... and it looks like several were not actually moved.
I only have 10k or so photos, but the thought of going through them manually fills me with dread.
If you can't offer help, commiseration's will do!!

I used this with great success on my Mom's iPhoto library that was a mess - and they have an Aperture version now!
http://brattoo.com/propaganda/#aperture
It's on sale and based on how well it worked in iPhoto I think I'm going to pick up a license.

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