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Factory ECU all the way. Integrating a factory ECU is usually not a very big deal. The only real difference between an after market controller and the factory unit is that the after market one comes with instructions (which may not be very good anyway,) whereas the factory unit comes with nothing. Much to the advantage of the factory ECU is that extensive documentation and wiring diagrams are available, and once it's installed, it will work with no further headaches.
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