The headache is probably caused by several things.
1. Eyestrain due to constant staring. A screen which emits light is much more tiring than a book which reflects light.
2. Flicker due to the scanning process. It doesn't matter how fast it scans, the flicker will get you. Use an LCD screen or a laptop. You'll notice the difference.
3. Not blinking. Your eyes will dry out very rapidly. Try something like Tears Naturale to lubricate them.
4. Keeping your head fixed in one position. Makes the neck muscles stiff.
5. Bad posture due to sitting position.

Try getting up every now and then. Look into the distance often while moving your head. Do a few exercises during a session. You could always take a couple of aspirins instead.

Bryan