i think the inner block would be much clearer and short as something like this (note also that $a and $b should be avoided because of their use by sort):

foreach (@FILE_ARRAY){
  next unless /^(?:([0-9_a-zA-Z*]+) +)?(?:([0-9_a-zA-Z*]+) +)?(?:([0-9
+_a-zA-Z*]+) +)?([0-9_a-zA-Z*]+)\((.+?)\)/;
  my ($args, @definition) = map { defined($_)?$_:'' } $5, $1, $2, $3, 
+$3;
  print join(" ", @definition) . " ARGS: $args\n";
}
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This only works with parsing one row

To workaround this, you need to slurp in either the whole file, or maybe just one function (maybe defined by /^}$/ ?? not going to be 100%) at a time.. Then your regex can use the /s modifier and span multiple lines and you'll want to change all the spaces in the regex to \s+

Later Im gonna add for parsing Perl scripts aswell, but that is alot easier.

easier? really? There is PPI, but there's set way to pass parameters into a function ... e.g.

sub foo {
  my $self = shift;
  my $p = {@_};
  my $name = $p->{name} or die;
  my $value = $p->{value} || 123;
}
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But there's many other ways (Super Search for threads on passing parameters) to do it, including mucking directly with @_