Stock springs have a shitty spring rate, and if you put them on a performance spring (its a stock replacement for performance) you will get that problem.

The shock is ment for aftermarket springs, Comon sense tells you that since they are dampaning adjustable.

and your top mount could of been worn out causing the 'clunking' which is comon with rubber upper mounts.

factory replacement meaning you dont need to modify anything to make them fit.