What fault codes do you have? If they are 0420 and 0430 they are catalytic converter efficiency codes which mean the rear O2 sensors need to be turned off. This would have nothing to do with the JBA brand or design for the headers, just a fact for all headers.
Also if you are using extenders for the front O2 sensors, stop immediately. Any loss of connection with the extenders can and will destroy the engine. The wiring harness for the front O2 sensors can be extended by releasing a tie-down at the top center of the bellhousing, eliminating the need for the aftermarket extenders.