If your input file isn't too big, you might want to slurp-and-split:

use strict;
use warnings;

my @scaffolds;
{ local $/   = undef;
  open(IN,"t.txt") or die;
  @scaffolds =  split(/(>scaffold\d+)\n/, <IN>);
}
close IN;

my $i;
my $s;
foreach (@scaffolds) {
   if (/^>/) {
      $s     = "$_.";         # assemble label for this scaffold
      $i     = 1;             # and initialize its counter
   } else {
      print    map { "$s." . $i++ . "\n"   # print incremented label
                           . $_            #   and the GACT* stuff
                   }
               split(/(?:N{4,}\n)+/, $_);  # for each entry within the
+ scaffold
   }
}
[download]

Sorry for changing all the variables on you. And one subtle detail worth noting is the parens in the first split!

Update:I changed the first split from split(/>scaffold(\d+)/, <IN>); to split(/(>scaffold\d+)\n/, <IN>);. This simplifies the assignment of $s and obviates the stripping of whitespace in map.