Can I re-install Apple's 'Mail' app in Mountain Lion?

I've seen similar posts, but none that quite match my dilemma.
I installed Mountain Lion over Snow Leopard 10.6.8
My mail account did not merge/migrate. By that I mean, no folders and no existing mail that was in those folders had populated themselves in my new ML Mail application.
   After much Google searching, I ended up just importing them from my latest Time Machine backup and now only those folders that had email in them in my last backup sit in "Import" in those specific folders.
Now tonight, my wife's iMac account on first opening it seems to be having no problem migrating her 1,000s of emails.
The only difference I can note is that upon opening Mail, there appears TWO (2) 'In-box' windows. I let hers run and they populated/migrated her old email into all of her existing folders.
My account on the other hand, I had closed the top-most 'In-box' window, thinking I had inadvertently tried to open 'Mail' twice.
Was it my closing that 2nd window in my Mail account that caused the migration to not take place?
Can I reinstall Mail and have it migrate itself - or is there a way to force migration? I'm not convinced my Time Machine backup has all email that was there, particularly if I only imported from 1 recent backup.
Thanks in advance for any help.

Could it be a possibility that this issue is somehow connected to my new router? I believe this problem started with the new router... So maybe there's a port issue or something?
***Edit*** 
Alright, so the problem seems to have been the router blocking port 993 which is used by the pop accounts. Look like it works fine now, it had to be added as an open port in the router configuration.

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