Perhaps the slowness you observe is in memory usage instead of the foreach loops. Instead of loading the entire file up into @project_module_list, read only one line of the file at a time. Replace your outer foreach loop with the following while loop and see if it improves.

open FH, "<database.txt" or die;
<FH>;   # ignore header line of CSV file
while ( my $project_module_list = <FH> ) {
  chomp $project_module_list;

  ## put remainder of code here

}
[download]