FWIW:
After working with the apple support folks, I believe we have solved my problem.
To repeat the symptoms:
-- updated from Snow Leopard to Lion
-- used a Time Capsule to install all my data on the new Mac
-- Opened Mail which had to reindex all my mail
-- During the reindex, there were a couple of places that things ground to a halt for an extended period
-- Mail quit after the index was complete
-- No matter what I did, I could not get a message viewer window to open up
We first tried removing the 3 Envelop-index files
-- quit mail
-- Finder:Go (hold down option key: LIbrary:Mail:v2:MailData
-- Move "Envelope-Index*" to the desktop, 3 files
-- start mail
--> this will reindex all your mailboxes, basically the same thing that happened the first time mail was opened
This did not work for me
We removed the Mail folder and then imported each mailbox one at a time
-- quit mail
-- Finder:Go (hold down option key: LIbrary
-- Move "Mail" folder to the desktop
-- start mail
Mail will ask you to enter one of your email accounts
-- A message viewer will open
-- send some test mails to yourself
-- Finder:Go (hold down option key):LIbrary:V2:Maildata
-- copy the Accounts.plist that is in the "Mail:V2:Maildata:Accounts.plist" to the above directory
-- Open Mail Preferences, all of your accounts should be present
FWIW: I found two versions of one account, one active and the other not. I deleted the active one
since it wasn't suppose to be active.
-- Send emails to each of your active accounts to ensure its working
Now you have to import each email account. You can do it all at once, but if something goes wrong
you may have to start all over again.
In Mail
-- File:Import Mailboxes
-- find the Mail folder you placed on your desktop
-- select Mail:V2:[IMAP-*|POP*]
-- the emails will all be found in an "Import" mailbox in Mail
-- Move the mails to the appropriate inbox (or whatever box)
-- Delete the Import mailbox
-- repeat the above for each account
Optionally, you can rename the Import mailbox to something else if you don't want to have to worry about
having an active account.
I'm pretty sure I lost some emails, but they were very old and I think they were the emails that were causing Mail to not work for me after the initial install.
If I decide it is important, I can mount my old sparse bundle and try to import those emails from there.
FWIW: in other posts, some folks found they could get things to work by just opening Mail over and over again.
I did not find that to work.