I had the same problem put the stock uca back on the car and the noise is gone.
Do a simple google search...
The 3.73 gear is 99% of your issue here. Pinion angle (with a stock drive shaft or an aftermarket one with a CV joint at the rear end) is not terribly critical as long as its close. Like Kelly said, by design they can operate smoothly at far greater angles than what we are subjecting them to. The new Jeep wranglers have the same type of joints and the operate fine at a MUCH higher angles with no noise.
Something is wrong with the 3.73 gears Ford produced. If you want to fix it, have a reputable shop replace them with another brand. The Ford Racing ones are just re-boxed production units and they will most likely make noise too.
My car has had the same gear noise as yours, 60-80 mph, since the day it rolled off the line. When I did the suspension it got way louder.