Thanks so much for the help again, I replace the sub input_data and sub output_data in original script with this and I get the following:

ACFX  28523  L           05/18/13  ABCCO    
ACFX  28523  L  05/01/13           ABCCO-C
[download]

I am pasting entire script, maybe I am doing something wrong, this is a little over my head, hopefully will begin understanding better

#!/usr/bin/perl
# 
use strict;
use warnings;
use Date::Calc qw( Delta_Days );

my %hashC=();
my %hash=();
input_data(1,'out1.txt');
input_data(2,'out2.txt');
#input_data(1,'pcarry.txt');
#input_data(2,'rcarry.txt');
output_data('final.txt');


#sub input_data {
#  my ($ix,$filename) = @_;
#  open FILE1, "<", $filename or die "$filename : $!\n";
#  while ( <FILE1> ) {
#    chomp $_;
#    my ( $key, $le, $date, $company ) = split ',', $_;
#    my $pk = join "\t",$key,$le,$company;
#    push @{$hash{$pk}[$ix]},fmt_ymd($date);
#  }
#  close FILE1;
#}
sub input_data {
  my ($ix,$filename) = @_;
  open FILE1, "<", $filename or die "$filename : $!\n";
  while ( <FILE1> ) {
    chomp $_;
    my ( $key, $le, $date, $company ) = split ',', $_;    
    my $pk = join "\t",$key,$le,$company;

    # remove -C from key and store
    if ($pk =~ s/-C$//){
    #  print "-C removed $pk\n";
      $hashC{$pk} = '-C';
    }
    
    push @{$hash{$pk}[$ix]},fmt_ymd($date);
  }
  close FILE1;
}

#sub output_data {
#  my $filename = shift;
#  open OUTFILE, ">", $filename or die "$filename : $!\n";

  # primary key
#  for my $pk (sort keys %hash){
#     my ($key,$le,$company) = split "\t",$pk;

sub output_data {
  my $filename = shift;
  open OUTFILE, ">", $filename or die "$filename : $!\n";

  # primary key
  for my $pk (sort keys %hash){
    my ($key,$le,$company) = split "\t",$pk;
    # add -C back if required
    $company .= $hashC{$pk} || '';


    # get multiple dates
#    print "$pk\n";
#   my @dates  = @{$hash{$pk}[1]};
#    my @rdates = @{$hash{$pk}[2]};
    my @dates  = (defined $hash{$pk}[1]) ? @{$hash{$pk}[1]} : ();
    my @rdates = (defined $hash{$pk}[2]) ? @{$hash{$pk}[2]} : ();
    
    # even up number of dates:
    while (@dates < @rdates) {
      push @dates,'1900-01-01';
    }
    while (@rdates < @dates) {
      push @rdates,'1900-01-01';
    }
    
    # print out multiple dates for each key
    for my $date (reverse sort @dates){
    
      # use match sub if more than 1
      if (@rdates > 1){
          @rdates = match($date,@rdates);
      }
      # rdates sorted so best match is first element
      my $rdate = shift @rdates;
      print join ' ',$key,$le,fmt_mdy($date),fmt_mdy($rdate),$company,
+"\n";
    }
  }
  close OUTFILE;
}

# match dates by calc days diff
# and sorting to get least diff
sub match {
  my ($date,@rdates) = @_;
  my @days=();
  # split date into y,m,d
  my @d1 = split /\D/,$date;
  
  # calc diff and store with date
  for my $rdate (@rdates){
    my @d2 = split /\D/,$rdate;
    push @days,[$rdate,abs Delta_Days(@d1,@d2)];
  }
  
  # sort array by days
  @days = sort {$a->[1] <=> $b->[1]} @days;
  
  # extract dates 
  return map {$_->[0]} @days;
}


# change mm/dd/yy to yyyy-mm-dd
sub fmt_ymd {
  my $mdy = shift;
  $mdy =~ s/ //g;
  my ($m,$d,$y) = split /\D/,$mdy;
  if ($y < 99){ $y += 2000 };
  return sprintf "%04d-%02d-%02d",$y,$m,$d;
}

# change yyyy-mm-dd to mm/dd/yy
sub fmt_mdy {
  my $ymd = shift;
  $ymd =~ s/ //g;
  return ' 'x8 if $ymd eq '1900-01-01';
  my ($y,$m,$d) = split /\D/,$ymd;
  $y -= 2000;
  return sprintf "%02d/%02d/%02d",$m,$d, $y;
}
[download]

I suggest you comment out this line temporarily
$company .= $hashC{$pk} || '';.

If you still get -C appearing in the output then check the data carefully for trailing spaces. You can also add the primary key into the output temporarily with separators like this to see spaces or other reason why they don't match up.

 print join ' ',$key,$le,fmt_mdy($date),fmt_mdy($rdate),$company,"|$pk
+|\n";
[download]

poj

thanks for that code I was able to fix my formatting and space issues so the appended file is the same field widths. I am still not getting the fields to match up.

ACFX  28523  L           05/18/13  ABCCO        
ACFX  28523  L  05/01/13           ABCCO-C      
ACFX  28526  L           05/28/13  ABCCO        
ACFX  28526  L  05/01/13           ABCCO-C      
ACFX  44866  L           05/28/13  ABCCO        
ACFX  44866  L  05/01/13           ABCCO-C      
ADMX  49266  L  05/03/13 05/16/13  PFGCO           
ADMX  63770  L  05/12/13 05/21/13  PFGCO           
ADMX  63975  L  05/12/13 05/30/13  PFGCO
[download]

the first and second row need to match (they do perfectly without the 
+-C) need them to look like:
ACFX  44866  L  05/01/13 05/28/13  ABCCO-C
[download]

I made sure file1 and file2 are both the same column widths, so now i just think the issue is with the company names not being exact...thanks