(Note that I have the .htaccess and php.ini file in that ConfigPath directory. I have presumed that's where they should be.)
Assuming that the code (pages) you're running are
in /archives, the .htaccess should be read and processed. You might confirm that .htaccess and php.ini are being read, by running the following script:
<?php phpinfo(); ?>
and see if changes you make to PHP settings show up. If they don't, something's wrong. Of course, this script must be in /archives, along with the PHP code you're trying to run.
Also, would fiddling with MySQL persistent connections solve my overall problem?
I doubt it, but that's not my area of expertise. Usually I think you would get an inability to connect or maybe a 500 error.