Recovering mail from hard disk failure

My hard disk was recently replaced after failing (at Apple's expense since my mac is still under warranty). Fortunately, I made a complete image of my old hard disk on an external drive just days before the problem arose, so am in the process of copying my documents, etc, to the new drive.
Still, I am having a number of problems, including in Mail. I can see my old mailboxes and messages on the external drive, and when I click on messages they open in Mail. I was able to copy the mailboxes to the Library on the new drive (and they appeared after closing and reopening the app), but the messages do not show up (ie the mailboxes are all empty).
To be more precise, I copied the mailboxes from the external drive to my new drive under username/library/mail/mailboxes. It appears that the messages are "there" (they appear in Finder under .../mailboxes/messages) and I can open them in Mail when I click on them from Finder. But the messages don't show up in the mailboxes within Mail.
Something else that might factor into this is that I use multiple email accounts. One reason I mention this is that I want to recover my 'sent' messages, regardless of which account the messages were mailed from.
Surely this is a fairly standard recovery problem but I can't find out a routine to make it work. Any advice would be greatly appreciated.
I would also be grateful for any pointers (ie other discussion threads) about how to reinstall apps (e.g. Acrobat) that I bought and downloaded, so do not have disks to use to reinstall.
PowerBook G4   Mac OS X (10.4.6)  

Hflint,
Try rebuilding your mailboxes from the mailbox menu (has to be done on each account, so expand the mailboxes with the small arrow in front of them).
the sent messages will all be in the mailboxes that correspond with each mail account, when you try to group them, you may loose the integrity of the Mail message database. In the Mail view window, when the send mailbox is collapsed, it will appear as if they are all in the same folder.
Try to open your Keychain access from your backup and see if there are certificates for Adobe in there, or look in Library/Adobe support
It is good practice to store all your license data e.g. in a mailbox folder for all software you download. Make sure you have good backups of such files because eventually they represent a lot of $$ and time to get it all restored.

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    Message was edited by: phantom 3444

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