The easiest way is to change your .* to be an appropriate negated character class or to use the ? modifier on the greedy * to make it less greedy.

1. print  $#{[$lines =~ /aaa[^b]*bbb[^c]*ccc\s*dddd/gsi]} + 1 . "\n";  # or ...
2. print  $#{[$lines =~ /aaa.*?bbb.*?ccc\s*dddd/gsi]} + 1 . "\n";

See the documentation in perlre and perlrequick and perlretut