Transfer emails from "On My Mac" to new Mac

Since the year 2001 I am saving all my personal emails, I like to see them maybe as a diary. Anyway, I keep them including attachments and cannot save them via iCloud - too big, too many. So I saved them “On My Mac”. Since I have two Time Machine backups I felt very comfortably about this.
Now I bought a new Mac and need to transfer the emails from my old Mac to the new Mac and have problems doing that. My local Apple store and Apple Care only offer the solution to transfer everything via migration assistant. Please just accept that this is no solution for me.
I know that this problem arouse here several times but unfortunately I cannot find an answer that works for me:
When I copy the corresponding mailboxes (Username) -> Library -> Mail (which really have all the mails inside because they are quite big in size) to my new Mac and additionally copy (Username) -> Library -> Preferences -> com.apple.mail-shared.plist I see the mailboxes on the new Mac, but they are all empty.
Furthermore I have an issue copying them at all, because the Library is only available after holding the option key and the window that opens shows only the active OS. So regardless if I connect my old Mac in Target mode, use a Time Machine backup or even copied the plist-file from my old Mac to an USB-stick - transferring it is difficult to impossible.
The funniest part, however: After I copied com.apple.mail-shared.plist into my preferences folder of the new Mac the appearance of my mailboxes in mails’s sidebar was weird, so I deleted it again (and the mailboxes including the saved emails) and assumed that after a restart Yosemite would create a new plist. But it didn’t! And my new Mac still runs fine - regarding the mails saved in iCloud - without this plist…
Any thoughts?

This causes problems for me. When I place a single .mbox file into a new folder and import that folder I get the following dialogue:
When I click 'continue' I get a new import folder, but the formatting is a garbled nightmare of seemingly random subdirectories upon subdirectories:
Each of the subdirectories under "ASV" should have just contained messages, not lots of embedded subdirectories. Am I doing something wrong?
P.S. I am trying to move mail from an iMac running 10.7.5 to a new iMac running 10.10.1

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Transfer emails from "On My Mac" to new Mac

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