Other starter comments:

1. When deleting parens from your string, you don't need /i; and I'm guessing you could replace them all before you split, like this?

   s/[()]//g;
   @t=split(/\t/,$_);
   [download]

2. Don't you want to reset $count? The easiest way to do that would be to put my $count; immediately below while (<IN>).
3. You could simplify your primary print statement like this:

   my $yn = ($count ge 3) ? 'Y' : 'N';
   print OUT join("\t", @t[1..4], ${yn}, $t[6..8]), "\n";
   [download]

   But are you overlooking the first element, $t[0]?