Problems displaying mailbox content in Lion Mail

OK I give up, and need help.  I have 10.7.3 installed on a late 2011 Macbook Pro 13" with 8gb of ram, running Mail 5.2.
I have tons of mail in various mailboxes, like 38 different mailboxes, with 39 sets of rules.  Some folders have 2000+ messages, but most have a couple of hundred in each with my inbox having about 200.  The issue is when I launch mail, and click on a mailbox, it can take up to a minute and a half to display the content.  Then I click on a different mailbox, it takes another minute or so.  Finally, I click on the previous displayed mailbox, and even though the data had populated a short time ago, it takes up to another minute and a half to display anything.  Originally I did an upgrade to Lion when it first came out from snow leopard, subsequently, I did a clean install on my 15" 2007 MBP with 3gb of ram, and it did not help.  I have been having this issue since the upgrade when Lion came out.  Then in February of 2012, my son went to basic training for the Army, and I took his 13" MBP to use.  I swapped hard drives, did an erase and reformatted with my drive (Hybrid 500gb SSD/regular SATA Drive) and did a clean install on my sons MBP, used the time machine to migrate all the data back over, and the problem continued.  I waited for the indexing to stop thinking that would fix the issue when done, but nope.  I have been a mac user since the early 80's and had an Apple IIe, so I feel a little defeated with this, but I have no idea what to do. Some of the things I have tried:
1.  Repair permissions
2.  Reinstall Lion again (not clean)
3.  Deleted preferences, reindexed mbox files and data.
4.  Clean Install of Lion and migrate.
5.  I give up...
Bill

It does not solve the problem, but may help for a future upgrade. I have been playing around with this, and note that if I select one storage folder for sent messages on my MAC, then select "classic layout" in the Mail preferences, then delete the field "From" from visualisation while leaving "To", then revert back to new layout (i.e. un-select classic layout, the messages are displayed as I'd like them to, i.e. with the "To" field.
BUT as soon as I click again on any other folder, say "Inbox" and then come back to the storage folder, the "From" field is there again and I only can see myself as the sender....

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