Mail Won't Open, But it's NOT "not responding"

This is the strangest thing I have seen.
Ok, let me start from the beginning -
A few days ago, my hard drive was starting to fail. Time Machine wasn't backing up from before that, even though it was set to run every day.
Last backup was done on 30 July.
So, When I saw the drive starting to fail, I manually backed up my mail so that none of it was lost.
The Apple guys replaced the HD yesterday. I started system restore at the last backup date on time machine, using Migration Manager. Everything seems to be there. I'm happy.
So before I open mail, I go and replace the files in Library > Mail >V2 with the files that I backed up.
I also replaced the com.apple.mail.plist in preferences file.
I try to open mail, it bounces a few time, put the little spotlight under the icon, but nothing happens. I left it for a few hours to see if it was maybe busy with something in the backend, but nada.
If I go to Apple > Force Quit, it pops up, but it does NOT say "not responding" next to it.
I have opened activity monitor, and it says 0,0 under CPU % - so to my mind that means nothing is happening.
iMac 27" mid 2010
OS X 10.9.4
2.8GHz Intel Core i3
16GM Memory, 1333 MHz DDR3
Any ideas?
I don't want to mess with this and break it more
Thanks!

Have you tried opening Mail from the Applications folder. The Dock alias may be corrupt.
Try a restart.
Do a backup, using either Time Machine or a cloning program, to ensure files/data can be recovered. Two backups are better than one.
Try setting up another admin user account to see if the same problem continues. If Back-to-My Mac is selected in System Preferences, the Guest account will not work. The intent is to see if it is specific to one account or a system wide problem. This account can be deleted later.
Isolating an issue by using another user account
If the problem is still there, try booting into the Safe Mode using your normal account. Disconnect all peripherals except those needed for the test. Shut down the computer and then power it back up after waiting 10 seconds. Immediately after hearing the startup chime, hold down the shift key and continue to hold it until the gray Apple icon and a progress bar appear. The boot up is significantly slower than normal. This will reset some caches, forces a directory check, and disables all startup and login items, among other things. When you reboot normally, the initial reboot may be slower than normal. If the system operates normally, there may be 3rd party applications which are causing a problem. Try deleting/disabling the third party applications after a restart by using the application un-installer. For each disable/delete, you will need to restart if you don't do them all at once.
Safe Mode - Mavericks
Safe Mode - About

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Message was edited by: Yann Roth

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