1) Smith is dead.
2) everyone is alive because the Smith virus, not the body, was destroyed. it is like at the end of m1, when Smith explodes and neo is left standing there.
3) yes
4) Neo is the only one who can reload it, and since he chose the other door, it wasn't reloaded. thence, there is a new version because of the Architect and Sati and Neo's sacrifice.