use strict;
use warnings;

my @hdr;
my @val;

for (;;) {
   my $hdr_line_in = <DATA>;
   last unless defined $hdr_line_in;

   my $val_line_in = <DATA>;
   last unless defined $val_line_in;

   chomp($hdr_line_in, $val_line_in);

   while ($hdr_line_in =~ /([^\s\d]+(\d+))/g) {
      my $hdr  = lc($1);
      my $row  = $2;
      my $skip = $-[1];
      my $val  = $val_line_in =~ /^.{$skip}(\S*)/ ? $1 : '';
      push(@{$hdr[$row]}, $hdr);
      push(@{$val[$row]}, $val);
   }

   last unless defined <DATA>;
}

foreach my $row (0..$#hdr) {
   next unless defined $hdr[$row];
   print(join(',', @{$hdr[$row]}), "\n");
   print(join(',', @{$val[$row]}), "\n");
}

__DATA__
A1             
9198 

B1   C1                          D1       E1    F1     
23   232                                        233     

G1                               H1        I1     
2222                                       323    

A2   B2      
1234 5678
[download]

outputs

a1,b1,c1,d1,e1,f1,g1,h1,i1
9198,23,232,,,233,2222,,323
a2,b2
1234,5678
[download]