Mail preferences cause lockup

I have a new Mac Pro (2 x 2.4 GHz Quad Xeon) with 24GB RAM and a 512 SSD, and have been having problems ever since getting it.
Current Problem:
If I try to view Preferences in Mail.app, I get the beachball of death. Force quit is the only solution at that point. The mail functions work fine, but I cannot change any settings, add or update any accounts, modify rules or any of it.
I've done the permissions repair, disk repair, PRAM reset, and LIbrary stuff of removing preferences and mail folders. This has not solved the inability to access mail preferences, though.
Background:
This is the second SSD after having hte first one replaced. Why? Because of cascading app crashes, and Lion would not reinstall. The Genius Bar restored my account on the new disk using a Time Machine backup from another disk on the machine. All seemed good for a while.
A second visit to the Genius Bar was to try to fix more crashes. Now there were secret permissions problems (that seem to override the normal chmod permissions on files and folders) preventing apps from starting up properly. It stumped him, and he was looking up arcane system-level commands to try to clean these issues up. The Genius spend 2 hours creating new users, migrating apps over, etc. I left with things seemingly fixed.
Also I have the same problem with Safari preferences when trying to set default browser. That gives me the beachball of death, too and the only solutio is to force-quit Safari.
Perhaps related: iCal randomly crashes. No spinner, just suddenly it's gone and a crash report is in its place.
Question:
Is there any way I can totally reset Mail.app to at least test if there's a permissions problem causing this? Or must I resort to wiping the SSD and reinstalling Lion from a DVD?

First, restore your Mail data. That's apparently not where the problem lies.
Please read this whole message before doing anything.
Boot in safe mode and log in as yourself. The instructions provided by Apple are as follows:
Be sure your Mac is shut down.
Press the power button.
Immediately after you hear the startup tone, hold the Shift key. The Shift key should be held as soon as possible after the startup tone, but not before the tone.
Release the Shift key when you see the gray Apple icon and the progress indicator (looks like a spinning gear).
During startup, you will see "Safe Boot" on the login screen, which appears even if you normally log in automatically. You must know your login password in order to log in. If you’ve forgotten the password, you will need to reset it before you begin.
Safe mode is slower than normal, and some things won’t work at all, possibly including wireless networking.
Launch Mail, and test again. Same problem now?
After testing, reboot as usual (i.e., not in safe mode.)

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    Dual 2 Ghz G5   Mac OS X (10.4.3)  

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