Your first problem is definitely the easiest. To loop over each line of the file, use while (<>) like so:
open my $outfile, '>', 'out.txt';
while (<>)
{
print $outfile $_ if /^(?:A id|M X)/;
}
close $outfile;
Obviously you may need a more rigorous regular expression, but this works for your example data. Your second problem is more difficult, so it'll have to wait for now.
Update: On second glance, your second probem is not well stated. What kind of comparison do you want to do? What should the output look like? Afraid I can't help with a poor problem statement.
print map{substr'hark, suPerJacent other l',$_,1}(11,7,6,16,5,1,15,18..23,8..10,24,17,0,12,13,3,14,2,4);
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