A handy module for your problem is Date::Parse.

#!/usr/bin/perl
use strict;
use warnings;
use Date::Parse;

while (<DATA>) {
    my ($name, $field1, $field2) = split /\s*#+\s*/;
    print str2time($field1), ' ', str2time(substr($field2,0,19)),"\n";
}

__DATA__
n1##Thu Oct 18 14:33:23 2007  ## 2007-10-18 14:33:23.000000000-0400
name2##Thu Feb  5 01:13:19 2009  ##2009-02-05 01:13:19.000000000-0500
name3##Sat Jan 24 10:03:37 2009  ##2009-01-24 10:03:37.000000000-0500
name8##Thu Feb  5 01:13:19 2009    ##2007-03-05 01:13:19.000000000-050
+0
[download]

The output is:

1192732403 1192732403
1233814399 1233814399
1232809417 1232809417
1233814399 1173075199
[download]