Your brake lighting and turnsignals should not have separate wires at the light housing. From what I gathered from your very confusing post there are separate wires at the lights and you spliced them together there.
I'm assuming you have the 7 wire switch. With this type of switch the brake light signal comes from the brake light switch to the turnsignal switch. Then it is directed in the turnsignal switch to the proper light.
I can't imagine why a harness built for turnsignals would have separate wires going to the rear for the brakes and the signals unless it was built for a 3 or 5 wire switch. If that is the case and you are using a 3 or 5 wire switch you need separate lights.
