Migrate mail from 10.6.8 to 10.7.5

Question

I have an extremely simple requirement, to manually migrate my mail from Snow leopard (10.6.8) to Lion (10.7.5). Explaining my situation below-
I have an iMac(originally 10.6.8) and for multiple reasons, I chose to upgrade to Lion (10.7.5) rather than Mountain Lion. From snow leopard I have taken each and every type of back in the form of the folders and attached prefernce files, for example, as a backup of keychains, I have the keychains folder from the main library as well as the user library, similarly for address book, safari and mail. So in case of mail, I have copied, the mail folder from the main library, mail and mail downloads folder from the user library and the com.apple.mail.plist from the preferences folder in the user library. After taking the said backups I have formatted my machine and installed the operating system lion, 10.7.5
Listing details of mail accounts, I have five live(Microsoft, live, outlook, hotmail, whatever you call them) accounts and one solitary gmail account. All these accounts are on POP protocol(simply because I want/need a copy of mails, communications and downloaded attachments to be on the mail server for emergency situations(such as this))
Now the issues begin, speaking strictly in terms of mail. Listing steps taken and their results,
1) Action - Followed the direct copy method listed in the link, (http://macs.about.com/b/2011/08/05/moving-your-snow-leopard-mail-to-lion.htm)
Copied the following folders, mail folder from main library(I.e. under macintosh hd), mail and mail downloads folder from the user library, com.apple.plist from the preferences folder in the user library. Note. a) this is a fresh install of lion, the mail app hasn't been executed even once. b) I deleted the v2 folder already located inside the mail folder in the user library, because it was suggested in the comments section in the link above.
Result - After the said process, I started mail(for the first time) mail detected the old structure, said it needed to reindex. After the process I could see all my accounts, all my mail, smart folders, all the attachments... Blissful. "BUT!!" when I hit get new mail, the mess begins. Mail starts to "RE" download ALL the mails AGAIN, 8000 mails, 7.5 gb worth of attachments.
2) Action - after the above debacle, quit mail and studied its folder structures in the user library as well as the main library, compared this folder structure of my snow leopard mail backup and manually tried COPYING ".mbox" in their respective new folder locations. Eg. Copied, "inbox.mbox" of account "x" from my snow leopard backup to the newly created folder structure in lion (I.e. inside the v2 folder, inside the account x folder.) also copied each individual preference file like MailAccounts.plist and all and copied them to their new location.
Result - the above process was an even bigger disaster. It corrupted my basic mail app. I had to perform an erase and reinstall the os.
3) action - after the fresh reinstall, and doing further research, I set up accounts INDIVIDUALLY (I.e. via Add account) this time "importing" each individual mailboxes via import command, once imported, I placed the emails contained within, to their respective inboxes.
Result - the above process too shows all my mails again, but when I hit get new mail, mail starts to redownload the **** mails from the server AGAIN!!
I have tried the above processes umpteen number of times in different variations, such as only one account at a time or importing only one inbox at a time. Still no luck. This a very frustrating issue. I have been manually migrating mail for the past 5 years. This new v2 folder is ******* everything up.
Note. Checked "duplicate mails" in lion help, which told me that duplicate mails get downloaded via the POP protocol if coming from an older version of OSx.
So is there a way I can make my mail lion compatible? Some software, some plugin? The entire world seemed to migrate mail, why not me?
A solution would be divine, as I am a designer with live projects and attachments stuck in the mail... Temporarily using mail from my iPad as my main machine which also has started acting like a ***** after ios 7, which is another headache all together.
Need help please, anyone on the forum with knowledge on how to solve this issue would have a special place in my heart besides a million thanks in advance.
Thanks a million in advance,
Abu Suda.

Answer 1

Try reindexing the mailbox. This can take awhile if you have a lot of mail.
Reindex messages.
If that doesn't work try deleting MessageUidsAlreadyDownloaded3.
Quit the application.
You need to look in your user Library. Either hold down the option key while using the Finder “Go To Folder” command and select your user Library in your home folder or use the Finder “Go To Folder” command and enter ~/Library/Mail/V2/Mail Data/MessageUidsAlreadyDownloaded3.  Move the file to your desktop.
Open the application and test. If it works okay, delete the file from the desktop.
If the application is the same, return thefile to where you got it from, overwriting the newer ones.
If you prefer to make your User library permanently visible, use the Terminal command found below.
Show User Library
You might want to bookmark the command. I had to use it again after I installed 10.8.5. I have also been informed that if you drag the user library to Finder it will remain visible.