Here's another option:

use strict;
use warnings;
use File::Slurp qw/ read_file write_file /;

$ARGV[0] or die "\nUsage: $0 <File>\n\n";

my $userlistContents = read_file $ARGV[0];

for ( grep /\S/, <DATA> ) {
    my ( $before, $after ) = split;
    $userlistContents =~ s/\b$before\b/$after/g;
}

write_file "changed_$ARGV[0]", $userlistContents;

__DATA__
JOE    JOHN
FRED    FREDERICK
SAM    SAMANTHA
[download]

Using File::Slurp is a nice way to get the file's contents into a scalar upon which global substitutions can be performed. The before and after names in the __DATA__ area are tab separated. Note that the changed file contents are written to the file named "changed_$ARGV[0]".

Hope this helps!