this part of yyour code confuses me:

 #get package name
  my $module = join ('::',$r->dir_config('RootNamespace'),
    split (/\//, substr($r->uri(),1,-3) ) );
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$r->dir_config returns CEMS::EXT so I dont see why you would want to join a string with ::. also the split of the URI doesn't look like your are leveraging the API properly. Perhaps

$r->filename
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is in order.

and finally, you can get rapid help with this from the modperl mailing list