1,WG0045068-DNA,A01,0,102186_A01_WTCCCT519791,...
2,WG0045068-DNA,B01,0,102186_B01_WTCCCT519793,...
3,WG0045068-DNA,C01,0,102186_C01_WTCCCT519805,...
1,WG0045066-DNA,A01,0,102176_A01_WTCCCT527545,...
2,WG0045066-DNA,B01,0,102176_B01_WTCCCT527498,...

##</code><code>##

WG0045068-DNA,A01,0,102186_A01_WTCCCT519791,...
WG0045068-DNA,B01,0,102186_B01_WTCCCT519793,...
WG0045068-DNA,C01,0,102186_C01_WTCCCT519805,...
WG0045068-DNA,A01,0,102187_A01_WTCCCT519791,...
WG0045068-DNA,B01,0,102188_B01_WTCCCT519793,...
WG0045068-DNA,C01,0,102187_C01_WTCCCT519805,...
WG0045068-DNA,A01,0,102187_A01_WTCCCT519791,...
WG0045068-DNA,B01,0,102188_B01_WTCCCT519793,...
WG0045068-DNA,C01,0,102186_C11_WTCCCT519805,...

and i want to get:

1,WG0045068-DNA,A01,0,102186_A01_WTCCCT519791,...
2,WG0045068-DNA,B01,0,102186_B01_WTCCCT519793,...
3,WG0045068-DNA,C01,0,102186_C01_WTCCCT519805,...
4,WG0045068-DNA,C01,0,102186_C11_WTCCCT519805,...
1,WG0045068-DNA,A01,0,102187_A01_WTCCCT519791,...
2,WG0045068-DNA,C01,0,102187_C01_WTCCCT519805,...
3,WG0045068-DNA,A01,0,102187_A01_WTCCCT519791,...
1,WG0045068-DNA,B01,0,102188_B01_WTCCCT519793,...
2,WG0045068-DNA,B01,0,102188_B01_WTCCCT519793,...

##</code><code>##

open (FILE1, "<", "filein.txt") || die "$!";
open (FILE2, ">", "fileout.out") || die "$!";
my $counter;
while(<FILE1>){
  m/.+,.+,\d+,(\d+)_.+/;
  $counter->{$1}++ ;
  print FILE2 "$counter->{$1},$_";
}
close FILE1;
close FILE2; 


result would be :
1,WG0045068-DNA,A01,0,102186_A01_WTCCCT519791,...
2,WG0045068-DNA,B01,0,102186_B01_WTCCCT519793,...
3,WG0045068-DNA,C01,0,102186_C01_WTCCCT519805,...
1,WG0045068-DNA,A01,0,102187_A01_WTCCCT519791,...
1,WG0045068-DNA,B01,0,102188_B01_WTCCCT519793,...
2,WG0045068-DNA,C01,0,102187_C01_WTCCCT519805,...
3,WG0045068-DNA,A01,0,102187_A01_WTCCCT519791,...
2,WG0045068-DNA,B01,0,102188_B01_WTCCCT519793,...
4,WG0045068-DNA,C01,0,102186_C11_WTCCCT519805,...

not sorted, but sorting should not be a problem :)

##</code><code>##

input.file
102186
102176

##</code><code>##


open (FILEIN, "<", "input.file") || die "$!";
my $counter;
while(<FILEIN>){
  $counter->{$_} = 0;
}
close FILEIN;

##</code><code>##

elsif($output eq "Inhouse") {
         
...

and here just implemente the counter. you can do the same thing for for previous decisions, if needed 
...
        
            else {
                $counter->{$save{$sam}{plateid}}++;
                print OUT "$counter->{$save{$sam}{plateid}},$save{$sam}{platename},$save{$sam}{well},$save{$sam}{case},$save{$sam}{plateid}_$save{$sam}{well}_$save{$sam}{clone},Homo sapiens,$save{$sam}{gender},,$save{$sam}{vol},50,$save{$sam}{extmethod},,0,$save{$sam}{father},$save{$sam}{mother},,$save{$sam}{source}\n";
            
            }
                
 ...