Hi, If I understood your question correctly, try this & see the Benchmark,

#!/usr/bin/perl

use strict;
use warnings;

use Benchmark 'cmpthese';

cmpthese(-1, {
    method1  =>  '&yours',
    method2  =>  '&new_one',
});


sub yours{

my %mapper;
open(MAP, "<map.ini");
while (<MAP>) {
     chomp;
     tr/A-Z/a-z/;
     my @map_line = split (/\t/);
     $mapper{$map_line[0]} = $map_line[1];
}
close(MAP);
 
open(IN, "<input1.txt");
open(OUT, ">input_new.txt");
while (<IN>) {
#print "%";
     tr/A-Z/a-z/;
     foreach my $key (sort keys %mapper) {
        s/\b$key\b/$mapper{$key}/g;
     }
     print OUT "$_";
}
close(IN);
close(OUT);

}

sub new_one{

open(MAP, "map.ini");
my $map = do{local $/;<MAP>};
close(MAP);
my %mapper;
$map = lc($map);
%mapper = map{split/\t/,$_} split(/\n/, $map);

 
open(IN, "input1.txt");
my $input = do{local $/;<IN>};
close(IN);

open(OUT, ">input_new.txt");

$input = lc($input);

foreach my $key (sort keys %mapper) {
  $input =~ s/\b$key\b/$mapper{$key}/g;
}

print OUT $input;
close(OUT);
}

__END__
          Rate method1 method2
method1  908/s      --    -13%
method2 1050/s     16%      --
[download]

I have check with less number of lines file only. You can check with your input.