You could save another few lines like this

#prepopulate copy error array;
sub popfilea {
  foreach my $ya ( 0 .. $gener ) {
    foreach my $xa ( 0 .. $total ) {
      $aoa[$xa][$ya] = (int rand(1+2*$copyerr)-$copyerr ) /$PCNT;
    }
  }
}
[download]

and here

sub popnum1 {
  ( $x, $y ) = @_;
  if ( ($y==0) || ($aod[$x][ $y-1 ] ne 'a') ) {
     return $initial + $aoa[$x][0];
  } else {
     return $aoa[$x][$y] + $aob[$x][ $y-1 ];
  }
}
[download]

moving the sprintf's to this line

 
$coper = sprintf '%.2f', popnum1( $x, $y )
[download]

or consider combining the two subs into one so that you have

 
$coper = sprintf '%.2f', popnum( $model, $x, $y )
[download]

hth poj