Use a 3/16 inch drill bit to make mounting holes in the flange that match the hole pattern in the servo. We could have 3D printed these... but hole patterns are a moving target.
Drill another hole about half-way up flange to secure the neck dowel in place.
Repeat these steps with the base flange and install the servo.
Extra screws left-over from micro-servos are great for holding the 12mm dowel in place. Hot-glue works nicely as well.
Make sure to check the height of the dowels as you go... the neck flange needs to be just above the hole at the base of the neck.
Grab some milk and cookies as a reward for your work so-far... you are in the home-stretch!