If you drill down in the ~/Library/Mail/V3 folder I assume if you go to the various mailbox folders (Inbox, Sent, etc.) and drill down further does your Time Machine have all the content there? In other words, did the content as least make it to Time Machine (especially important since you no longer have the old Mac, and since they are POP and don't exist on the server anymore presumably).
The mail folder structure is separated by accounts with a folder name of a GUID (i.e. 1bcd1fb3a-3525c-3627156-162512356c) so even if these are POP emails from an email service you no longer have you can transplant them to an active account you actually have set up.
You can sort out those individual emails files and say, put them on your Desktop, then drag them into your current Mail App structure to import them. If you have dozens of Mailbox folders in a complex hierarchy this would be cumbersome but doable, if you have a fairly simple hierarchy in your Inbox this manual process wouldn't be too time consuming.
If you've confirmed Time Machine actually has the content you could also try importing the Mac user account from Time Machine using Migration Assistant to see if that has better luck handling it than Time Machine did.