I fixed my issue, though it took hours of trial and error.
First, check Console (Applications/Utilities/Console) and click on All Messages in the left sidebar. I had a message about permission denied to copy a file during the upgrade. I manually moved that file to the desktop. After that the message migration finished, and Mail launched. Hurray I thought! But on reboot, Mail would not launch. It just hung. This time there weren't any helpful messages in Console to be found.
I read over these threads for the tips:
https://discussions.apple.com/thread/3189986?start=0&tstart=0
https://discussions.apple.com/thread/3191534
As best I can remember (it's been a long night), this was my process:
(Force) Quit Mail
Navigate to userI/Library/Mail folder
Move the entire Mail folder elsewhere, like your desktop
Launch Mail. At this point it should be be prompting you for info.
If you don't have anything on your machine only, just put in your info and download everything from your server from scratch. You're done! If however you have my problem with 164,000 messages stored locally, read on…
Quit Mail
Back in user/Library there's a new Mail folder.
One by one, move the items from the old Mail folder to the new one and launch Mail. Make sure to move the user/library/mail/v2/maildata/accounts.plist first so it stops prompting you for account info. Make sure to quit Mail between every file move. If you don't see a v2 folder, or a v2-temp folder, it means the migration hasn't happened yet. Just keep moving things over until it does, cause the migration changes the directory structure of the Mail folder.
At the point you move your old archived messages over, the next Launch Apple will import and migrate all the messages. This can take anywhere from 2 minutes to 45 depending on how many messages it needs to cull through.
I ended up moving everything but the RSS folder items back, and Mail is once again stable.
At some point I also booted into Lion Recovery partition (hold Command + R at boot) and ran Disk Utility to repair permissions. However I don't believe that actually helped.
Good Luck!