Steps to setup - some ideas.
1. UCI compliance or not. And you are allowed one morphological exception. I think this has been discussed in previous posts in this thread.
2. Knee tracking. This is controlled by cleat position and foot angle left/right and is an important setup. Every other setup point is less important until one is making adjustments for lower CdA. Wedges are sometimes placed in shoes to adjust knee tracking.
3. Seat height. In general, it is going to be higher than the road position.
4 Seat fore and aft. In general, the seat position is moved forward and up as the body is rotated toward the handlebar.
5. Once the saddle is set, the aerobars are lowered until the back is essentially flat.
6. At this point, the angle between the thigh and knee as the pedal goes over the top is measured and the crank length adjusted - usually shorter than the road cranks.
7. The stem is then adjusted to position the arm angle and this is where one needs someone with experience to look at side view and make changes.
8. The space between the arms is adjusted to make it narrow as possible with the proviso that narrowing the distance between the arms does NOT cause the head to pop up.
9. Finally, the angle of the aerobar extensions is adjusted so the tips of the bars are 10 cm above level.
This completes the setup and then the rider is tested for CdA and all adjustments other than cleat position are tweaked.
In the end, the rider may not be able to make much power in this position and it may take months of strength and adaptation to generate power in the optimized time trial position.