Mail didn't migrate when I went from Snow Leopard to Mountain Lion

Just got a new MacBook Pro with Retina.  It came with Lion on it, I upgraded it to Mountain Lion.  Then, I used Migration Assistant to bring over everything from my Time Machine.  My old MacBook Pro was running Snow Leopard. 
The big glitch seems to be Mail.  The mailboxes and folders are in the user/Library folder, but when I open up Mail, it shows I have about 400 emails instead of 50,000+.  And, none of the Rules, Smart Mailboxes, etc. are there.
Would migrating to Lion first and then upgrading solve this?  Is this a known problem with ugrading from SL to ML?  Should I just move the Mail folders in place and try again (I've done this before and am comfortable with the command line)?
I'm sure there are clever ways of rebuilding it all by hand, but I'd love to avoid that.
Thanks!

I ended up calling Apple Tech Support for help on this.  Got directed to a Mail expert.  He had me move the following files from my home Library file folder.
~\Library\Mail\V2\MailData\Envelope Index
~\Library\Mail\V2\MailData\Envelope Index-shm
~\Library\Mail\V2\MailData\Envelope Index-wal
Then he asked me to quit Mail and then restart it again.  When it restarted, it imported the mail (which the original migration had not done before).  This solved about 90% of the problems.  In my old mail folder in Snow Leopard, I had a Mail folder called Archive.  Since this is now a reserved folder name, the import to Mountain Lion choked and it created five duplicates of this folder and its subfolders.  I just deleted these and then went to Time Machine and brought in a single copy.  The Rules and Smart Folders I had were gone and couldn't be resurrected, so had to spend some time and rebuild them by hand.  But, now it all seems to be working well.

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