As an underweight, under-muscled teen (no offense, just laying it out), I don't really think a low-carb diet is the best idea.
However, if you don't "feel" well with certain carbs, we can certainly work around it to some extent.
There are plenty of carb sources other than "grains." Beans, white/red/sweet potatoes, Ezekiel bread, and quinoa would be a few things to look into.
In the two weeks you've been following Dan John's plan, how much bodyweight have you gained? That's going to be the best answer as to whether you're holding yourself back or not.
Have you been trying to follow the basic nutrition plan Dan laid out in that article?...