Problems moving mailboxes to new Mac

I decided not to use the Migration assistant when I got my new Mac Pro - I installed all the software from scratch to make a nice clean installation. However, to move all of my mail across I simply copied the Mail and Mail Downloads folders from Library. I have the user folder and the hard drive named the same on my new Mac as on my old one.
It certainly looked like it had worked fine. But a few days on, I was trying to search for an old email which contained a font I needed, and discovered that the email was completely blank - and all others in the same mailbox were also completely blank. Oddly, the attachment was actually present in the Mail Downloads folder - but I'm concerned that the emails aren't actually there.
Fortunately the content is all still present on my old computer - so what is the best way to move all of my mail to my new Mac? Please note that I have about 4 inboxes for different email accounts, and some of my mail gets automatically moved to various mailboxes in the 'on my mac' section.

I copied the Mail and Mail Downloads folders again, and this time I also copied com.apple.mail.plist and com.apple.mail.searchhistory.plist. It now seems to be all there, I cannot spot anything missing. Are there any more files (preferences etc) that I should have copied?

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