Mail Disappeared after 10.2.8 to 10.4.3 upgrade

I just upgraded to Tiger. I started Mail and waited for everything to import from previous Mail. (I didn't backup old Mail folders...).
Then I opened my new Mail (2.0.5) and realized I was missing mail from my POP accounts. I closed Mail and backed up my POP account folders to another harddrive. Then I tried to find a solution at this forum but no thread I could find has my problem exactly. I have too many folders/files and I don't know which ones to delete and in what order... My rebuilds do nothing...HELP!!
This is what's in my largest POP folder (997Mb) (backed up):
Deleted Messages/Drafts/Junk/Sent Messages/INBOX.mboxes
MessageUidsAlreadyDownloaded file
MessageUidsAlreadyDownloaded2 file
This is what's in my INBOX.mbox (408Mb):
info.plist (8k)
mbox (227.7Mb)
mbox.SKindex (179.7Mb)
mbox.SKindex.isValid (0k)
Messages Folder(empty)
Messages-T0random-string Folder (13 messages)
tableofcontents (448k)
If anyone could help I would really appreciate it!
Thanks,
Theo
G4 450 Mac OS X (10.4.3) G4 450, 768 RAM, Plenty of HD
G4 450 Mac OS X (10.2.x)

Theo,
My earlier reply was somehow lost by the servers. Please read the following articles for background, and post back:
http://docs.info.apple.com/article.html?artnum=301315
and
http://docs.info.apple.com/article.html?path=Mail/2.0/en/ml807.html
Be sure to maintain a copy of everything, until resolved.
PowerMac G5 Dual 2.5, iBook, and QS G4 867 Mac OS X (10.4.3)

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