This worked with the sample data. It uses strict and warnings. There are 5 additional lines and changes to 4 lines. Otherwise, the code is the same as yours. Not saying there may be better ways.  :-)

#!/usr/bin/perl
use strict;
use warnings;

my @data;    # new addition
my $max = 0; # new addition
while (<DATA>) {
    chomp;            # new change
    next unless /\S/; # new change

    my $string = $_;  # new change
    $string =~ s/,000//g;
    $string =~ s/,//g; 
    my @numbers= $string =~ /(\d+)/g;
    my $f= $numbers[0];
    my $s= $numbers[1] || 0; # new change
    my $isf9 = substr($f,-3);
    if ($isf9 =~/999/) {$f=$f + 1;}
    my $iss9 = substr($s,-3);
    if ($iss9 =~/999/) {$s=$s + 1;}
    $f =~ s/000//g;
    $s =~ s/000//g;

    my $fac;
    
    if ($f>0 && $s>0){ $fac = (($s-$f)/2)+$f;}
    if ($f>0 && $s<1){ $fac = $f;}
    if ($fac>0)
    {
        my $length = length($fac);        # new addition
        $max = $length if $length > $max; # new addition
        $_ =~ s/^/($fac) /;
        $_ =~ s/$/;fac=$fac/;
     }
    push @data, $_;       
                
} 

# new addition
print map {s/\((.+?)\)/ sprintf "(%$max.1f)", $1/e; "$_\n"} @data; 

__DATA__
Less than $10,000 
$10,000 to less than $20,000 
$20,000 to less than $30,000 
$30,000 to less than $40,000 
$40,000 to less than $50,000 
$50,000 to less than $60,000 
$60,000 to less than $70,000 
$70,000 to less than $80,000 
$80,000 to less than $90,000 
$90,000 to less than $100,000 
$100,000 to less than $125,000 
$125,000 to less than $150,000 
$150,000 or higher
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