my %config = (
   CONFIG_PCI => 'y',
   CONFIG_BSD_PROCESS_ACCT => 'y',
);
while (<>) {
   if ((my ($n,v) = split/=/) == 2) {
      if (my $new_value = $config{$n}) {
         print "$n=$new_value\n";
         next;
      }
   }
   print;
}
[download]

Note that, with the config extract provided by OP,

# CONFIG_HOTPLUG_PCI is not set
[download]

doesn't match your split, which would prevent the value from being set if needed.

So, what have you tried?

Sounds like you want to open the file, read its contents into a hash, muck about with those contents, and write the contents back out. You might find that Tie::File will do the trick for you.

my %config_settings = (
  CONFIG_NET => 'y',
  CONFIG_HOTPLUG => 'y',
  # whatever else you want to set
)

open(KERNEL_CONFIG, '<', '/usr/src/linux2.4/.config');
open(NEW_CONFIG, '>', '/usr/src/linux2.4/.config.new');
while my $config_line (<KERNEL_CONFIG>) {
  $config_line =~ /([A-Z0-9_])/;
  $config_line = $1 . '=' . $config_settings{$1} . "\n" if exists $con
+fig_settings{$1};
  print NEW_CONFIG $config_line;
}
close KERNEL_CONFIG;
[download]

Update: Initially forgot to include the \n when constructing a new $config_line.