I concentrated on just getting your script in bounds. So far, so good. The first thing that you want to do is to check and double-check for errors, warnings. Look for simple things such as:

Have you declared all your variables?
Are all your subroutines defined?
Are your variables properly scoped?
Have you checked for anything redundant?
Is any part of your code unreachable?
(Can it be removed?)

Second, you must know exactly what your variables, subroutines, packages, and modules used are. module_info will tell you exactly what you are doing. For example, I ran module_info -a on your script: 
Name:        /root/Desktop/rework.pl
Version:     v2.0.0
Directory:   
File:        /root/Desktop/rework.pl
Core module: no

Modules used:
    English
    File::Spec
    Getopt::Std
    IO::File
    Switch
    Time::HiRes
    autodie
    strict
    version
    warnings

Packages created:
    main    1312019949.17447

Subroutines defined:
    main
        assign_headers
        assign_names
        check_params
        get_fields_plan
        get_params
        trim

[download]
Third, run some checks to see how bad the damage is:). 
perl -c script.pl
perl -w script.pl
perl -MO=Lint script.pl
perltidy script.pl

[download]
Here's your script as I fixed it, minus the file part: 
#!/usr/bin/perl

use strict;
use warnings;
use File::Spec;
use Getopt::Std;
use IO::File;
use Switch;
use Time::HiRes qw(gettimeofday tv_interval); 
use version 0.77; our $VERSION = qv("v2.0.0");

use English qw(-no_match_vars);
local $OUTPUT_AUTOFLUSH = 1;

print my $timer_start = gettimeofday(), "\n";
my(%inputs) = ();
my(%params) = ();
getopts('o:r:p:t:n:f:g:d', \%inputs);
die "Error Getting Parameters\n" 
    unless get_params(\%inputs, \%params);
check_params(\%params);

my $outfile = 
    File::Spec->catfile($params{'outfolder'},$params{'rootname'});
my $outnamefile = 
    File::Spec->catfile($params{'outfolder'}, $params{'rootname'} );
my $outlinecount = $outfile . '_db_proc_linecount.txt';
$outfile = $outfile . '_db_proc_data.csv';
$outnamefile = $outnamefile .  '_db_proc_names.csv';
print "Output SSS File: $outfile\n";
print "Output Names File: $outnamefile\n";

my $hdrmap;
my(%hdr_types) = (
    fields  =>\&get_fields_area, 
    regions =>\&get_fields_region,
    plan    =>\&get_fields_plan
);
die 'Unable to match sss type. ' 
    unless defined($hdr_types{$params{ssstype}});
$hdrmap = $hdr_types{$params{ssstype}}();
my $namemap = get_fields_plan($params{ssstype});

#open I, '<', $infile or die "Unable to open file $infile.\n";
open my $O, '>', $outfile or die "Unable to open file $outfile.\n";
open my $ON, '>', $outnamefile or die "Unable to open file $outnamefil
+e.\n";
#open OLCT, '<', $outlinecount or die "Unable to open file $outlinecou
+nt.\n";

foreach (my $i=0; $i<3; $i++)
{
    my $line = <$O>;
    chomp ($line);
    $line =~ s/^\s+//;
    $line =~ s/\s+$//;
    my @sp = split (/\s+/,$line);
    
    foreach (my $j=0; $j<scalar(@sp); $j++)
    {
      my @hdrs;        
        @hdrs = $hdrs[$j] . q{} . $sp[$j];    
    }

}
print "[" . join(",", my @hdrs) . "]\n";
foreach my $hdr (@hdrs){
    trim(\$hdr);
    print "CHECKING HEADERS ------------\n";
    }
    foreach my $key (sort keys %{$hdrmap}) {

     my ( $index )= grep { $hdrs[$_] eq $hdrmap->{$key}[0] } 0..$#hdrs
+;
     if (defined ($index)) {
          $hdrmap->{$key}[1] = $index; 
          print "HEADER MATCH: " . "\t" . $key . "\t" . $hdrmap->{$key
+}[0] . "\t[" . $hdrmap->{$key}[1]. "]\n";
     }
     else {
          print "HEADER NOT FOUND: " . "\t" . $key . "\t" . $hdrmap->{
+$key}[0] . "\n";
    }
}
print "-----------------------------------------------\n";

my @flist = ();
my @fnamelist = ();
assign_names($hdrmap, \@flist);
assign_names($namemap, \@fnamelist);
print "[" . join(",", @flist) . "]\n";
print $O join(",", @flist) . ",RUN_ID\n";
print $ON join(",", @fnamelist) . ",RUN_ID\n";
exit();

my $l_units = <$O>;
chomp ($l_units);
print "UNITS -- > [$l_units]\n";    

use autodie qw(:close);
close($O);
close($ON);

sub get_params {
    my $inr = shift;
    my $pr = shift;
    $pr->{'debug'} = 1;        
    $pr->{'runid'} = -1000;    
    $pr->{'filter'} = ".*";
    $pr->{'datefilter'} = "";
    $pr->{'filename'} = "NA";
    $pr->{'outfolder'} = ".";
    $pr->{'ssstype'} = "";    
    foreach my $key (keys %{$inr}) {
         $pr->{'debug'} = $inr->{$key} if $key eq 'd';
         $pr->{'runid'} = $inr->{$key} if $key eq 'n';
         $pr->{'filter'} = $inr->{$key} if $key eq 'f';
         $pr->{'datefilter'} = $inr->{$key} if $key eq 'g';
         $pr->{'filename'} = $inr->{$key} if $key eq 'r';
         $pr->{'outfolder'} = $inr->{$key} if $key eq 'o';
         $pr->{'ssstype'} = $inr->{$key}    if $key eq 't';
    }
    return 1;
}

sub check_params {
    my $pr = shift;
    die "Require RunID if not in debug mode\n" if ($pr->{debug} == 1 a
+nd $pr->{runid} == -1000);
    (-e $pr->{filename}) or die "Unable to find input filename: $pr->{
+filename}\n";
    (-e $pr->{outfolder}) or die "Unable to find outfolder: $pr->{outf
+older}\n";
    $pr->{filter} = ".*" if $pr->{filter} eq "";
    my ($volume, $dirs, $rootname) = File::Spec->splitpath($params{fil
+ename});
    $rootname =~ s/\.sss$//;
    
    my @sp = split(/_/,$rootname);
    $params{rootname} = $rootname;
    $params{ssstype} = $sp[-1] if $params{ssstype} eq "";
    print "Run Parameters: \n";
    foreach my $key (keys %{$pr}) {
         print "$key -> [$pr->{$key}]\n";    
    }
    return 1;    
}

sub get_fields_plan {
    my $tblFields = shift;
    $tblFields->{'DATE_EN'} = ["__________ __________ Date",-1];
    $tblFields->{'HEADER1'} = ["Header1 Header1 Header1",-1];
    $tblFields->{'HEADER2'} = ["Header2 Header2 Header2",-1];
    $tblFields->{'HEADER3'} = ["Header3 Header3 Header3",-1];
    $tblFields->{'HEADER4'} = ["Header4 Header4 Header4",-1];
    $tblFields->{'HEADER5'} = ["Header4 Header5 Header5",-1];
    $tblFields->{'HEADER6'} = ["Header6 Header6 Header6",-1];
    return $tblFields;    
}

sub assign_headers {
    my $hdrmap = shift;
    my $headline = shift;
    my $sptagref = shift;                        
    $$sptagref = '\s*,\s*' if $$headline=~ m/,/;
    
    my @hdrs = split(/$$sptagref/, $$headline);
    foreach my $hdr (@hdrs){
    trim(\$hdr);
    print "CHECKING HEADERS ------------\n";
        }
        foreach my $key (sort keys %{$hdrmap}) {
            my ( $index )= grep { $hdrs[$_] eq $hdrmap->{$key}[0] } 0.
+.$#hdrs;
                 if (defined ($index)) {
                      $hdrmap->{$key}[1] = $index; 
                      print "HEADER MATCH: " . "\t" . $key . "\t" . $h
+drmap->{$key}[0] . "\t[" . $hdrmap->{$key}[1]. "]\n";
       }
         else {
              print "HEADER NOT FOUND: " . "\t" . $key . "\t" . $hdrma
+p->{$key}[0] . "\n";
         }
    }
    print "-----------------------------------------------\n";
}

sub assign_names {
     my $hdrmap = shift;
     my $flist = shift;
     @$flist = ();
     foreach my $key (sort keys %{$hdrmap}) {
         my $i = $hdrmap->{$key}[1];
          push(@{$flist}, $key) if ($i != -1);
     }
}

sub trim {
     my $sref = shift;
     $$sref =~ s/^\s+//;
     $$sref =~ s/\s+$//;
}

[download]

In reply to Re: Space delimted to CSV, Index and data extraction loop by Khen1950fx
in thread Space delimted to CSV, Index and data extraction loop by SixShot

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