Problems with sent box, reindexing mail

Question

I am in the middle of a mail crisis and in need of help.  I apologize for the longwinded explanation, but I thought I would be thorough in the hopes that it will help me get help.
It started with my sent box (which is very large) "dragging" when I ran searches in it (which I often have to do with my work).
Firstly, I tried to rebuild the sent box.  Mail froze halfway through the process and I had to force quit it.  When I started mail again, I noticed that the content of the messages were not correlating to the right message headers (recipient or subject line).  I tried rebuilding the sent box again.  This time, it went a little farther before freezing (it froze when the activity window indicated something was being done with the attachments - I can't remember exactly what).  After force quitting again, I noticed that the messages in the sent box were correlating properly but it was stil very slow in searches, the box took a real long time to open, and sometimes it would freeze mail.
I then tried to reindex mail as per instructions found on the apple site: quit mail, go to the mail data folder, remove the envelope foldes, and re-start mail, which would cause mail to have to import the messages again.  I made sure I did a back to up prior to trying this.  When doing so, my time capsule accused that it didn't have enough space, and that is when I first noticed that my HD was bown up to near its capacity; strange, I thought, but proceeded to erase some media to make room so I could finish the back up.  The importing/reindexing started and all was moving along fine until it got to the (now evil) sent box...  it froze.  I tried a couple of times, and it kept freezing. 
I tried to go back to where I was before reindexing by erasing the new envelope folders that had been created, and replacing them with the ones that were there before and I had removed.  It seemingly worked as Mail started again.  However, now had more issues.  First, my inbox was empty...  I had to restore it from time machine back up.  Then, I noticed that the content of the messages in all of my mailboxes would not load.  I could see the messages and their previews, but the content would not load when I clicked on the messages.  All of that on top of the sent box conitunuing to misbehave. 
By this time, I started getting messages from the OS about my startup disk being almost full (real strange since I had just freed up close to 80 GB!).  I knew something was wrong with that, but went ahead and got rid of another 30GB so I could proceed with trying to fix mail and would come back to this problem later.
I decided to try the reindexing again.  Tried the terminal method, but nothing seemed to happen.  Tried the replacing of the envelope folders again, and the same happened:  froze and my HD went to capacity again.  I then realized that the reindexing and the filling of the HD had to be directly connected.  After some research, I downloaded an app (whatsize) to find heavy or duplicate files, and, sure enough, there were hundreds of GB in duplicate mail data (sent box) in my library.  The Whatsize app is currently working to sort out all of the duplicate files (a 20 hour process).  This is my first time using this app, but I am thinking that, upon conclusion, I should be able to delete the duplicates...
That brings to where I am at now.  Where to go from here?  After (if) deleting the duplicates, what is the best way to restablish Mail?
Any help will be much appreciated as I cannot work without Mail.

Answer 1

In the Finder, go to ~/Library/Mail/. With that folder open, do Edit > Select All (⌘A), then Edit > Copy (⌘C), and paste it in your reply to this post, to let me see the names of the files and folders present at the root level of the Mail folder.
Before actually posting that information, you may edit it so that the file/folder names do not reveal any details you wish to keep private, e.g. you may replace any real username with "username" to hide your real email address if you wish; similarly, you may disguise any domain names you don't want to be revealed. Try to be consistent in how you disguise those details, though, as we may need to refer to them in subsequent posts.
Now, go to ~/Library/Mail/Mailboxes/. With that folder open, repeat the process to let me see the names of the files and folders it contains. Again, you may disguise any mailbox names you wish to keep private. Be careful to not alter any suffixes, though.
Finally, for the two accounts involved in the problem, locate the account folders within ~/Library/Mail/ -- their name begins with the account type (POP, IMAP, Mac), followed by the account username and the incoming mail server. For each account folder, repeat the process to let me see the names of the files and folders it contains.
Note: For those not familiarized with the ~/ notation, it refers to the user's home folder. You can easily locate any of the folders referred to in this post by copying the file path here, doing Go > Go to Folder in the Finder, and pasting the file path there.