I made an improvement to my script and I thought Id post it so that others can benefit from it.
This rewritten version gives me two files... items that were "found" when searching the allper array and items that were "not found".
(PS: the variables were renamed)

foreach (@raw_data)
{
$item=$_;
chomp($item);
if (grep/$item/,@allper)
{
push(@found,grep/$item/,@allper);
}
else
{
push(@notfound,$item);
}
}

open RESULT, ">_found_items.txt";
print RESULT "@found\n\n";
close(RESULT);

open noRESULT, ">_doesnotexist.txt";
print noRESULT "@notfound\n\n";
close(noRESULT);