Update: I didn't see demerphq's Read more tag. This doesn't add much if anything to what he said. Mea culpa.

I don't have time to comment on the whole thing, but thought a comment on the following piece of code might be useful to you:

my $filename = "";
$filename = $hash{"LIS_FILE"} if($node eq "sam");
$filename = $hash{"LIS_FILE_TEST"} if($node eq "cad2");
chomp $filename;
my $htmfilename = "";
$htmfilename = $hash{"HTM_FILE"} if($node eq "sam");
$htmfilename = $hash{"HTM_FILE_TEST"} if($node eq "cad2");
chomp $htmfilename;
my $sqt_path = "";
$sqt_path = $hash{"SQT_PATH"} if($node eq "sam");
$sqt_path = $hash{"SQT_PATH_TEST"} if($node eq "cad2");
chomp $sqt_path;
my $database_name = "";
$database_name = $hash{"DB_NAME"} if($node eq "sam");
$database_name = $hash{"DB_NAME_TEST"} if($node eq "cad2");
chop $database_name;

my $mail_server_name = "";
$mail_server_name = $hash{"MAIL_SERVER"} if($node eq "sam");
$mail_server_name = $hash{"MAIL_SERVER_TEST"} if($node eq "cad2");
chomp $mail_server_name;
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First, Where did %hash come from? I am assuming that it is a by product of the read_config($node); call. It would be more obvious if you commented this, or even better ( IMO ) made read_config($node); return a hash-ref.

Second, it seems that you have take a liking to post_conditionals. Each of these pairs could be rewritten as if {} else {} constructs. With the dual post-conditionals you are forcing the evaluation of both conditions every time, potentially doubling your work.

Third, there is a pattern to what you are doing in this block -- refactor it. One suggestion is:

my $postfix = '';
if ( $node eq 'cad2' ) {
   $postfix = '_TEST';
}

my $attrlist = { filename => 
                    $hash{"LIS_FILE${postfix}"},
                 htmfilename => 
                    $hash{"HTM_FILE${postfix}"},
                 sqt_path => 
                    $hash{"SQT_PATH${postfix}"},
                 database_name => 
                    $hash{"DB_NAME${postfix}"},
               mail_server_name => 
                    $hash{"MAIL_SERVER${postfix}"}
                };
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Now obviously your information is stored in a hash and will change the way you refer to the data -- but you could set it up so that you have scalars:

my ($filename, $htmfilename, 
    $sqt_path, $database_name, 
    $mail_server_name) = ('', '', '', '', '');
my @refs = (\$filename, \$htmfilename, 
            \$sqt_path, \$database_name,
            \$mail_server_name);

foreach my $attr ( qw( LIS_FILE HTM_FILE SQT_PATH 
                       DB_NAME MAIL_SERVER ) ) 
{
    my $store = shift @refs;
    $$store = $hash{"${attr}${postfix}"};

}
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Of course this method will lead to a coupling between the @refs and list of fields to be gathered. As well, this code does not test whether the desired %hash entry exists. Including that you might get:

my ($filename, $htmfilename, 
    $sqt_path, $database_name, 
    $mail_server_name) = ('', '', '', '', '');
my @refs = (\$filename, \$htmfilename, 
            \$sqt_path, \$database_name,
            \$mail_server_name);

foreach my $attr ( qw( LIS_FILE HTM_FILE SQT_PATH 
                       DB_NAME MAIL_SERVER ) ) 
{
    my $store = shift @refs;
    if ( defined $hash{"${attr}${postfix}"} ) {
       $$store = $hash{"${attr}${postfix}"};
    } else {
        die "Missing required config data: ${attr}${postfix}";
    }
}
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