Replace your shocks, factory shocks (which are probably worn out unless you have a newer car) were definitely not made to support a stiffer spring rate, so they do a bad job of dampening the kinetic energy coming out of the springs. Just remember, shocks convert kinetic energy from the springs into heat energy inside the shock, you want a shock that can handle the load the spring puts out.
EDIT: The scraping wont go away, you lowered you car, you just have to pay more attention now. I've found taking speed bumps at an angle if at all possible helps.