The break in procedure is critical to brake performance. The reason for a proper break in is to establish an even layer of friction material deposited on the rotors from the brake pads. It is very important that this initial layer of friction material is evenly distributed.
5 moderate to aggressive stops from 40 mph down to 10 mph in rapid succession without letting the brakes cool and do not come to a complete stop. If you're forced to stop, either shift into neutral or give room in front so you can allow the vehicle to roll slightly while waiting for the light. The rotors will be very hot and holding down the brake pedal will allow the pad to create an imprint on the rotor. This is where the judder can originate from.
Then perform 5 moderate stops from 35 mph to 5 mph in rapid succession without letting the brakes cool. You should expect to smell some resin as the brakes get hot.
After step 2 is complete, drive around for as long as possible without excessively heating the brakes and without coming to a complete stop (try for about 5 minutes at moderate speed). This is the cooling stage. It allows the heated resin in the brake pads to cool and cure.
After the brakes have cooled to standard operating temperature, you may use the brakes normally.