unless the ecu was tuned for GTR sized injectors it will be no better than the stock ecu. also what sort of chip is in the ecu? is it one of those powerchip type ones that you can't tune? if so, they are a major waste of time and money. if it is something that has been tuned by a tuner and you can have it retuned then you should be able to take it to a tuner and have them simply change the injector size to the GTR size in the settings (depending on ecu setup) and then you will be able to atleast run the car, however you should still get it fully tuned once you have the car on the road as you may end up damaging the motor if the tune doesn't suit your car.
generally "stage X" stuff when it comes to ECU's are a load of crap. they are usually just generic tuned stuff and won't give the power gains of an individually tuned ecu, since it will be done specifically for your car. if you walk into a workshop and asked a tuner to give your car a "stage 3 tune" you'd find that it is more than likely the exact same tune as you would get if you asked for a stage 1 tune, lol. a tuner simply tunes an ecu to be at a certain AFR and timing that isn't going to make it ping.