Netlist ECO tool Gates On the Fly can do the job easily. You can use perl compatible script like following to add an AND gate to each D pin of each flop.
my @ffs = get_cells("-type", "ff", "-hier"); # Get all flops
foreach my $ff (@ffs){
my @dpins = get_pins("-input", "-data", $ff);
foreach my $pin (@dpins){
change_pin($pin, "AND2X2", "", "some_enable,-");
}
}