Use the throttle for maintaining your engine speed, not the choke, as the choke doesn't connect at the same spot as the throttle. That and when you are riding you use the throttle anyway, not the choke.
DAMHIK. BTDT.
You want to use cyl #3 as your fixed reference as the throttle cable is connected to it direct and not adjustable.
From there you can set 3 to 4, then 3 to 2 and then 2 to 1. That's if you are using a TwinMax.
If you have a 4 port Carbtune, still use #3 as your fixed reference. Then set the remaining ones the same. 3 to 4, 3 to 2 then 2 to 1.
If you make too much of an adjustment to #4 make sure to check your TPS setting when you are finished.
And to your question, yes there are only 3 screws.