Now, I've looked into using PerlSetVar, PerlSetEnv and PerlPassEnv. The problem is, these directives only seem to work when called through Apache via a browser. But when Apache is initially loading, Apache does not seem to pass any of this information to modules as it is loading them.

Use PerlSetVar the usual way:

PerlSetVar foo bar

Then in your startup.pl file, access them like this:

my $config = Apache->server->dir_config('foo');

On a side note, it's best if possible to stay away from PerlSetEnv/PerlPassEnv, because setting up the environment at request time is costly. If you don't use the %ENV at all in your modules then you can save some cycles by configuring PerlSetupEnv Off.

Just to add some spice to the this problem, I definitely would like to keep the solution to this within the httpd.conf file.

Check out Perl Sections: you can directly set yourp ackage variables from httpd.conf:

<Perl>
  $My::Config::foo = 'bar';
</Perl>
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