# Somewhere in your Makefile.PL...
use ExtUtils::MakeMaker qw(prompt);

# Prompt the user for the system ID, offering "Default_id"
# as the default (ie, if they just hit enter without 
# entering any new text)
my $system_id = prompt("What is the system ID", "Default_id");

run_code_to_update_system_id_in_all_files( $system_id );

##</code><code>##

/usr/bin/update_system_id.pl new_system_id