Sounds like you have a lot of poor planning from the previous support person to amend. (doesn't seem wise to keep custom scripts under the perl directory)

Figure out all the non-core modules you need by parsing all your scripts, who cares what .pm files are actually installed..you just care about the ones being used. Then download the .ppd and .tar.gz files for each module from the appropriate site(s).

After that write a script to automate the installation of all those modules. You'll need to modify the path within the .ppd file to match that of the locally installed/copied .tar.gz files.

ActivePerl is pretty simple to install silently, check the docs for exact syntax/options. In the environment I work we use SMS(ugh), so I have an SMS issuance that installs perl itself and then runs my script to install the extra modules. I do something like this to install Perl itself:

msiexec.exe /I blah.msi TARGETDIR=D:\PERL AddPerlToPath=NO /q
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and my install script for the modules that runs after perl itself is installed is like this :

use PPM;
....
   # array of fully qualified path to each .ppd file
    for ( @modules_to_install )
        {
        print "Attempting to install $_\n";

        if( PPM::InstallPackage("package" => $_) )
          {
          print "Successfully installed $_\n";
          }
        else
          {
          print "Failed to install $_\n";
          $errors++;
          }
      }
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Note: I wrote my automated module install script before ppm3 came about, so there may be newer ways/abilities to do this. After thousands of successful installs it has worked very well. If the server was healthy enough for Perl itself to install from the .msi file then the module install script always ran successfully for me.