Where you have 
if ($sid eq $sidtwobinder[0])

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you are not getting a match because $sid is "1" and $sidtwobinder[0] is "sid 1" (note the two spaces between sid and 1). You could change your @sid array to contain the whole text. I don't know how big your dataset is but it is inefficient to loop through @unpairedSidBinder inside the outer loop. You could split it into two stages, saving the matches in a hash of arrays - something like: 
my @sid = ('sid  1','sid  2','sid  7','sid  9');

my %hoa;
foreach my $el (@unpairedSidBinder){
    my ( $key, $data ) = split /\|/,$el;
    push( @{ $hoa{$key} }, $data );
}
foreach my $key (@sid) {
    my $ary = $hoa{$key} or next;
    my $temp = join(" ", @$ary );
    print "$key|$temp\n";

}

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In reply to Re: concatenating elements of an array in twos by tangent
in thread concatenating elements of an array in twos by Sandy_Bio_Perl

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