Mail: Consolidate multiple mail folders

I have been using macs for as long as I can remember. I used to use Eudora and eventually migrated to OS X Mail and imported my data. Needless to say I have a lot of emails now. The problem is sometime last year I had an issue with OS X Mail and made a couple backups of my mail folder data (poorly planned). Now I have two or three copies of mail folders which do not contain a full set of data.
Does anyone have suggestions on how to consolidate the multiple OS X Mail data sets into a single set? I don't care about the folder structures I have. I just want to ensure I have a full set of received and sent mail with as few duplicates as possible.
I tried importing all folders into a fresh 10.9 Mavericks install using Mail but for whatever reason (5 days later...) it almost doubled the size of the original folders. Normally, I wouldn't care as I had a 1 TB disk in my MBP. But I just got a new Haswell MBP with just a 256 GB drive. Space is at a premium.
I searched the internet and even the discussions here without much luck. There was reference to an AppleScript that would highlight duplicates but that tool doesn't seem to be working any longer.
Thank you,
Jonathan

Thanks for replying. Sorry, I didn't explain what I did clearly enough. I literally made copies in the Finder of my ~/Library/Mail folder... so I have three folders of roughly 20 GB (yes, 20 GB!!) each at different stages of completeness. I could MAYBE just use one but I'm not comfortable doing that quite yet if there is a different solution. When I imported, Mail took 5 days and the new ~/Library/Mail folder is 145 GB. I haven't a clue what it did to inflate it so much.
I'm probably a crazy hoarder (ok, definitely) but when I have emails back to 1996 or something it's hard to not at least try for full population.
I tried Mail Store Home (suggested by Steve Gibson @ GRC.com) and it was great. It pulled in a ton of emails (into proprietary database IIRC) and I exported to EML. But OS X Mail imports in a fashion that creates a zillion folders. Also not helpful.
I'm also dealing with 201,000 emails, manual anything isn't ideal... I'm absolutely a hoarder.

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