in reply to mod_perl application structure

How/Where are you preloading the modules? Are you using Apache::DBI? If you are make sure it is loaded before any DBI calls including the loading of.

Setup perl-status
<Location /perl-status> SetHandler perl-script PerlHandler Apache::Status order deny,allow #deny from all allow from all # adjust for your IP </Location>
and preload Apache::Status BEFORE Apache::DBI, if you haven't already. That will allow you to confirm that Apache::DBI is caching the DBI connects and you can see what modules are loaded into memory.