10.5.1 Mail crashes OS (black screen) then wipes Mail settings + mailboxes

Question

So I dragged a PDF to the mail icon to start a new message, Mail creates new message body with PDF but then crashes the entire OS - press the on/off to reboot your system.
Then when the OS comes up again the entire Mail settings are wiped.
Okay so I do a restore from the archived Mail.
Spaghetti Mail results.
I've now got two sets of archived Mail (this is a new MacBook so I recently imported old Mails from the iBook) nested inside multiple folders... one set of the original iBook to MacBook import - and now a set of the MacBook mail with a set of the iBook to MacBook import inside it.
Problems I have with this: -
1. Mail crashed my MacBook in the first place
2. Mail forgot the mail settings even though the mailboxes are still in ~/me/library/mail
3. Mail double imported archived mail
4. Mail has no clear and easy way to merge old mail back into a new mail setup.
Now I'm going to resync from the IMAP mail servers to get my INBOXes back... so multiple multiple nests of spaghetti.
This is pretty unacceptable behaviour.
Solution: -
1. Mail should have a back up set of settings to "Clone" settings and mailboxes from an archive
2. Mail should be smart enough to know that the mailboxes in the users library/mail folder are not alien entities but the data it needs to work.
3. Mail should have a way to merge archives into the current set of live mail boxes - SENT especially important.
Now I'll be resyncing then dragging and dropping to try to get it to some normality.
Yes perhaps Time Machine is the answer - but that does not resolve the cloning of settings issue... nor help when moving from 10.4
Awful

Answer 1

Okay - so I've begun restoring the email accounts - I have 5 of them... and it seems to be recognising them and importing the mail from the existing set of mailboxes I'd imported already.
However there is still the issue of Mail recognising that those Mailboxes exist. It should know that they are there and offer to set up the accounts using these mail boxes as a basis.
Not very smart to do it the way it has been done - now I need to delete the archives I've just imported... but that scares me so perhaps I'll just live with them as they are...
Not very impressed with the recovery process.