Here is the problem I am getting in a nutshell.
Pretty Permalink + Main Domain = Site goes down Immediately. MySQL gets hammered.
Pretty Permalink + Sub-Domain = Site is up
No Permalink (default links) + Main Domain = Site is up.
My pretty permalinks use the very standard Redirect rules for wordpress into the .htaccess file (I haven't touched this file).
For example, my site is mydomain.com. For months, my staging domain was on staging.mydomain.com. I was using the pretty permalinks on this site to access content: staging.mydomain.com/project/my-project.
When the launch date came, I switched staging to main domain by changing the path in my httpd config file to point the main domain to the staging server path. And the site went down immediately - MySQL gets hammered.
If on the main domain, I change the permalinks to default, the site stays up.
I have researched this topic a lot, and I am no closer to a solution.
I would much appreciate any help!