I'm not sure CPAN.pm will understand line 4, specifying where your MyConfig.pm file is. Try removing this line, and simply put the MyConfig.pm file in your $HOME/.cpan/CPAN/ directory.

A couple of other points to check:

• sometimes CPAN.pm expects directories like INSTALLMAN3DIR=~/share/man/man3 to already exist, so you may have to initially create them.
• you should verify that the paths to the specified programs, such as /usr/bin/make, are the correct ones. You may be able to just specify these by name (without the full path) if your PATH environment variable is appropriately set.

UPDATE
Another possibility you might check is that the user that the cgi script is running under may have a different HOME environment variable than you do. If that's the case, it may be easier to set the CPAN.pm config options directly in the script, as in the following:

use CPAN;
use strict;
use warnings;
$CPAN::Config = {
  'build_cache' => q[10],
  'build_dir' => q[/full/path/to/your/build/dir],
# etc
  'makepl_arg' => q[PREFIX=/full/path/to/wherever
                    LIB=/full/path/to/lib/perl5
                    # etc
                   ],
# etc
  'wget' => q[],
};
$CPAN::Config_loaded = 1;
my $mod = 'GD';
my $obj = CPAN::Shell->expand('Module',$mod);
$obj->install;
[download]

#! /usr/bin/perl -w

use strict;
use CGI;
use CGI::Carp qw(fatalsToBrowser);
use CPAN;
use CPAN::Config;

my $query = new CGI;
my $update = $query->url_param('update');
my $moduleparam = $query->url_param('module');

if ($update) {
    for my $key (keys %{$CPAN::Config}) {
        $CPAN::Config->{$key} = $query->param($key) unless grep($key e
+q $_, qw[dontload_hash urllist wait_list]);
    }
}

else {
    $CPAN::Config->{'build_dir'} = q[EDITED FOR SECURITY PURPOSES];
    $CPAN::Config->{'cpan_home'} = q[EDITED FOR SECURITY PURPOSES];
    $CPAN::Config->{'histfile'} = q[EDITED FOR SECURITY PURPOSES];
    $CPAN::Config->{'keep_source_where'} = q[EDITED FOR SECURITY PURPO
+SES];
    $CPAN::Config->{'make_install_arg'} = q[];
    $CPAN::Config->{'makepl_arg'} = q[PREFIX=EDITED FOR SECURITY PURPO
+SES SITELIBEXP=EDITED FOR SECURITY PURPOSES LIB=EDITED FOR SECURITY P
+URPOSES INSTALLMAN1DIR=EDITED FOR SECURITY PURPOSES INSTALLMAN3DIR=ED
+ITED FOR SECURITY PURPOSES INSTALLSITEMAN1DIR=EDITED FOR SECURITY PUR
+POSES INSTALLSITEMAN3DIR=EDITED FOR SECURITY PURPOSES];
}

print $query->header();
printf '<h2>CGI CPAN Module Installer</h2><h3>CPAN Configuration (CPAN
+::Config)</h3><form action="%s?update=1&module=%s" method="post"><tab
+le border="0" cellpadding="3" cellspacing="0">', $query->url(-relativ
+e=>1), $moduleparam;

for my $key (sort keys %{$CPAN::Config}) {
    printf '<tr><td align="right"><label for="%s">%s</label></td><td><
+input type="text" name="%s" value="%s" size="75" /></td></tr>', $key,
+ $key, $key, $CPAN::Config->{$key} unless grep($key eq $_, qw[dontloa
+d_hash urllist wait_list]);
}

print '<tr><td colspan="2" align="right"><input type="submit" value="r
+un again" /></td></tr></table></form>';

if ($moduleparam) {
    print '<p /><h3>Working...</h3><textarea cols="76" rows="25">';
    my $module = CPAN::Shell->expand('Module',$moduleparam);
    $module->install;
    print '</textarea><p />';
}

print '<strong>finished</strong>';
[download]

GD.pm requires the gd library to be installed - do you know if it's available in some standard location? Also, the perl Makefile.PL stage prompts the user for some information on how the library was compiled; for a non-interactive install, you should verify that that defaults are appropriate.

I've found that many times, the very best thing to do in a case like this is to instantiate Human::Conversation and talk to the admin of the box. They might not have any problem, especially if you offer to help out.

It pays to ask.