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]

and verify that the appropriate permissions are in place to allow the script to install things in the specified locations.