How to manually restore emails in Lion?
Put the contents of the mail directory in /Users/yourusername/Library/Mail (or ~/Library/Mail in other words)
com.apple.mail.plist goes to /Users/yourusername/Library/Preferences (~/Library/Preferences)
Firstly copy the com.apple.mail.plist from the backup to the user library (~/Library/preferences) and it does ask to replace, just click yes.
Secondly copy the mail folder to the user library (~/Library) and when complete, just open mail as normal.