It looks like the drill bit your using is far too big. You should mark out the point you need to drill carefully with the images in the jungleflasher tutorial and use a 08-1.0mm drill bit.
What i do is use a 1mm drill bit, and twist it by hand on the point. That way it takes longer but i find i am able to control how deep it goes by how hard i press.
If your not very comfortable with that, an easy way to do it is to get a kamikaze template and drill bit. There made to be virtually idiot-proof.