What is down
 

On the interception and run back if a players shoulder is touching the ground is he down. Because the player shoulder was clearly touching the ground in the Enzone while the ball was not?

Obviously it wasn't clearly otherwise they would've overruled the call on the field that it was a TD.

It was a TD. The players head, not shoulder, hit first, and from all angles that they provided, it appeared that the ball broke the plane. There were no 100% conclusive angles or shots to prove otherwise.

Sometimes part of our brain interprets what the eye "sees" in a way that another part of the brain wants it to be interpreted. Perhaps that is what happened to you?

You mean the part of the brain that has enough alcohol in it? Sorry, couldn't resist, late at night, I'm usually not like this.

To answer your question, yes a player would be down when his shoulder hit the ground. At that point the position of the ball would determine whether a touchdown is scored or not. The experts found that the ball broke the plane of the goal line prior to the runner being down.

For the record, the NFHS (High School) rule states; (NF:4.2.2.a) "The ball becomes dead and the down is ended (a) When a runner goes out of bounds, is held so his forward progress is stopped or allows any part of his person other than hand or foot to touch the ground." The NCAA (College) and NFL (Pro) rules regarding this issue are similar.

There is an "exception" to this specific sub-section that allows for a place kick holder to have his knee(s) on the ground. The NCAA and NFL rules also provide for this exception although the details vary somewhat.

As suggested above, it's important to realize that although football is often referred to, "as a game of inches", it's also a game of angles.