This strikes me as a diagnosis of exclusion. There's no reason to think caffeinated beverages are killing our kids. You can get some idea of what he ingested with a toxicology report, but the amounts given in the article fall in the normal/safe range (in my opinion).
It reminds me of this style of headline: "Kid Dies When Struck by Baseball in the Chest."
The LD50 of caffeine in humans is dependent on individual sensitivity, but is estimated to be about 150 to 200 milligrams per kilogram of body mass or roughly 80 to 100 cups of coffee for an average adult.
Say the kid weighed 50kg (set low to be conservative). That's an LD50 at 200mg X 50 = 10 grams. Not gonna happen with the beverages described. Was he super sensitive to caffeine? Maybe. Stuff happens.