Actually, it should be And the more tightly he controls where the chakra goes and how much of it he uses, the fewer headaches he gets, and that's worth the whole training by itself.

'Less' refers to a numberless amount, while 'fewer' deals with hard numbers. Say I have five pounds of sugar. If you take away two pounds, then I have fewer pounds of sugar, and less sugar overall. It's a subtle distinction that is slowly eroding from spoken English, but it still matters in written English. (Fifty years from now, the difference between the two words will probably be gone altogether, but that prospect depresses me so we shall not speak of it. *sigh*)