If you still have a tune that is set up for the factory injectors, it is going to run very poorly with the larger injectors in it.
The reason it takes a bit for the roughness to start is because it is waiting for the o2 sensors to heat up and start making corrections. Once that happens, the corrections are made based on stock injector data in the tune.
I would recommend putting the stock injectors back in for the break in miles, and then letting your tuner get the new ones dialed in when the time comes for a tune.
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