Alright man, youre mixing too many things up.
The secondary butterflies are only there to smooth out throttle response. Your bike should be able to idle normally and hit redline even with those removed. Since you have them unplugged in the fully open position, they should not restrict the engine from making max power....or affect the idle.
To make it easier to troubleshoot the issue, I would advise completely removing the secondary butterflies from the engine.
The Idle adjustment Knob: All this does is keep the throttle body valves slightly open....depending on how much u adjust it. When u turn the knob, it pushes a little pin further out, which pushes on a tab, causing the throttle bodies to stay slightly open. Turn it the other way and it does the opposite. Its a very simple mechanism.
Now, does the engine hit redline when u are in neutral?