whenever you modify a car, it's always in your best interest to maximize the modification's output by making adjustments. vaguely and generally speaking it's always good to be tuned to your set up. however the ecu also adapts short and long term fuel trims/timing advancement in small adjustments based on weather/temperature changes. i would think if you could just clear the adaptations it already has and get it to relearn it to your new/improved set up, that would be ideal. but most likely it'll just monitor the fuel trim via your pre-cat oxygen sensor(s) and adjust itself on it's own.

porting the intake manifold might not even result in a power gain if the intake ports on the head are still smaller or not evenly matched anyways. just don't **** up your intake lol,
gl,
Dave =]