One, F-22 doesn't have 3D. Only 2D. It can't affect the Yaw axis.
3D is in 3-paddle TVC or in a Direct-Nozzle-Control TVC system.
Moving on, here's how I see it:
Fighter
Controls operate normally, turret controlled by hat switch on stick
GERWALK
Throttle controls downward thrust
Foot pedals control forward thrust (Ties in with later dynamic in Battroid)
Left Stick(Throttle with stick axes unlocked) controls the left arm
Right Stick controls the right arm
Turret controlled by hat switch on right stick
Battroid
Throttle controls downward thrust
Foot pedals control walking (Works on dual-motor control theory; pressing the left pedal moves the valk around the right leg as a pivot, vice versa, and both moves forward)
Left Stick controls left arm(Throttle with stick axes unlocked)
Right Stick controls right arm
HMD controls the turret
Really, the controls are simpler than they're made out to be.
The hard part is a throttle assembly that opens to 45 and 90 degree angles, both of which unlock a set of stick axes in the joint, the whole thing mounted to the sliding throttle mechanism. It would not work on a rotary throtttle.