TuneEcu is wrong when it says to sync throttles with No2. No1 cylinder at the front end of the bike is the master as it has the throttle cables connected to it.
You will need either TuneBoy or Tune ECU
As you adjust the balance screws it changes the value of the TPS which makes the idle stepper adjust the idle speed and causes the readings to change. If you adjust the idle to 1000 rpm to remove the influence of the idle stepper motor then it becomes quicker and easier because the only thing influencing the readings is the adjustment made by your screwdriver. You can either tape the twistgrip to hold the speed at about 1000 rpm or adjust the cables, tape is the best option.
Adjust No2 to the same value as No1 then adjust No3 to the same value as the other 2. rev the bike a bit then check it , you may have to adjust again slightly but with care you can get each reading exactly the same. Untape the throttle. Look at the way the readings move in relation to each other with a settled idle, they will all now be the same but one throttle may lag behind another as they react to idle speed hunting very slightly. Usually No3 is behind the others and may need a small increase of adjustment. This last check of the way the throttle reading move in relation to each other at idle will make the bike even smoother, especially with small throttle openings as in slow traffic.
Easy with the RAMAIR filter fitted. A pain with the original plumbing on because refitting the plastic ducts can move the throttle bodies and mess the adjustments up.
I've done this on lots of rockets and it works a treat but please don't use number 2 as the master throttle or you will get in a mess. Look at the picture in the Tuneece link above and you will see the error. No1 is the one which the cables open, No2 follows what the shaft coming out of No1 does then No3 does what No 2 tells it to.