A 9V battery in a backpack is orders of magnitude less dangerous than a cell phone in a backpack. 9Vs can get hot enough to smoke. LiPo can get hot enough to explode. Yet we put up with cell phone batteries by the dozens in every classroom.

In this case the wires and boards were unsecured and could easily have shorted, unlike in a cell phone. Had he plugged it in there's an unprotected transformer floating around in the case.

You're missing the fact that the kid brought in a project for a class, got credit for that project, and was told "don't show that to anybody" by his teacher.

Wait, is that true? Nothing I've read said anything about it being a project.

And then, rather than having anyone ask that teacher about the pencil case full of clock parts, the school district called in five cops.

You missed the part where the kid continued to show the clock to others and then set the clock to go off during another class after being told not to show anyone else.

Not the bomb squad, mind you.

No, because the kid was trying to cause a disruption with a suspicious device, not with a bomb.

Doesn't the whole incident seem suspicious? The kid's behavior, the response, it really seems like there's more behind the story and I wouldn't be surprised to find out that the kid has been disruptive in a similar manner before. It's the only explanation that makes any sense.