1. Yes, from what I've read, Bilsteins use internal bump stops.
2. The end of the coil does NOT line up with the little notch in the lower spring perch. It is very deceptive, but you just ignore the notch in the lower spring perch for the most part, and instead you worry about the oval shape of the spring and spring perch which should line up better.
3. The shock is fine where it is, and doesn't drop out the bottom. This varies between dampers designs.
4. The proper way to tighten the top nut is using an allen key and a somewhat specialized deep wrench. Tightening the top nut with an impact wrench is pretty bad for the seals of the damper, but this is the way most people do it.