Please use <code> code goes here</code> tags, it improves readability a lot;)

Your not far away, lets take a fresh look and decompose the problem, for example like:

1. reading of a config file
2. reading of user input
3. writing/updating of the config file

As a general comment put use strict; use warnings; in your scripts.

#!/usr/bin/perl 
use strict;
use warnings;

my %config; 
my $filename = "TestConfig.cfg"; 

open ( FILE,'<', $filename) or die "Cannot open file: $!"; 

while (<FILE>) { 
    chomp; s/#.*//;     # no comments 
    s/^\s+//;           # no leading white 
    s/\s+$//;           # no trailing white 
    next unless length; # anything left? 
    my ($var, $value) = split(/\s*=\s*/, $_, 2);
    $config{$var} = $value;
    
} close FILE;

while(my ($key, $value) = each(%config)) {
    print "key: $key, value: $value\n";
}
[download]

I used the following config file:

ServerIP=<10.11.200.189> 
FirewallIP=<10.11.200.189> 
WebServerListenPort=<5566> 
ConnectionStartPort=<9400> 
ConnectionEndPort=<9419> 
RecordServerIP=<10.11.200.189> 
MediaPort=<7080> 
ControlPort=<7081>
[download]

Make sure you understand what happens. Why is the 2 used in the split function?

2. Reading of user input

You are on the right way. There are more ways to do it, I would probably use a module from CPAN, but using STDIN should work fine.

3. Writing of the config file

You open the file for * reading * only:) You can work with a temporary file and later overwrite the original or do the update in-place.

HTH

Cheers

Harry