Throttle body #1 is your base.
Page 3-17 of the S1 Yamaha manual explains the procedure.
Yamaha calls for a certain pressure # to try to obtain however, I, being at sea level couldn't get close to it.
As long as you can adjust your idle (up and down), are at approx. 3/4 a turn out (for #1), adjust away.
Note, the adjustment is VERY touchy and adjusting one cylinder WILL affect another. I use a large commercial fan in front of the radiator/engine as I do fine tune, see below, (which takes time).
The initial setting is usually about 3/4 a turn out, adjust the others accordingly to even them up.
Factory spec's allow for up to 10 mm's difference however the closer the better. I would also recommend holding the throttle at 4k and re-adjusting. That alone helps with vibs. Re-adjust at idle and get a good average.
Pic of my recent TB sync after a valve adjustment:
Had to adjust #4, both exhaust valves (too tight by .001"):
