On Friday I upgraded to Lion on my G5.
All went well except for the mail program. I have had similar difficulties that have already been mentioned. The short story is the mail program was "migrating" data for over 15 hours.
I followed the suggestions:
(1) Delete anything with envelope in the ~/Library/Preferences/apple.mail.com of Mail folders.
(2) I then went into my Time Capsule backup prior to the Lion upgrade and dragged out the Mail folder, saving it to my Desktop
(3) I tried several times to open and "migrate" the file into mail - it continued to "hang" for hours, i.e., with no resolution
(4) In the meantime I checked my email via my Firefox for my three mail accounts - a bit of a hassel but its a work around and my archives stayed intact with all three accounts - mostly.
(5) Next I highlighted my Mail Folder which I had copied to my desktop, see (2) above. I clicked on "File" and "Get Info" and studied my options - out of curiousity and with nothing to lose in the "Get Info" window I checked a box that said "use 32 bit". I then closed the window.
(6) I shutdown the computer and even unplugged it for 60 seconds trying to get a full reset.
(7) Powering back up, I clicked on the Mail Icon selected Continue for install and then the migration happened very quickly and I heard the "ding" that the migration was in process or complete(?)
(8) The Mail program window opened looking very familiar and for about another 30 minutes the migration of data populated into the program. I did not try to compose emails. I wanted to allow the program to run and populate the archive of the various email accounts. Everything is intact at this time.
Now I am sending, receiving emails without difficulty.
I do not know which step really solved this issue - it may have been the full reboot, which is more absolute than the computer restarting after the update. It may have been the "32 bit" box checked in Get Info while the Mail Folder on my Desktop was highlighted. The Genius' in this forum may be laughing at that strategy, its okay, I am just glad it worked. And I empathize with those whose Mail program is still not working.
I hope something here helps.
*Apple really needs to make this crystal clear and be transparent about the issues when offering an upgrade. This is not the first time an OSX upgrade has caused problems with the Mail Program. My suggestion is that Apple upgrade the Mail Program first then add all the sexy bells and whistles. If we don't have a Mail Program that integrate withing the upgrade - "Houston, or rather Cupertino, we have a problem!"
Good luck people.