The stock sub is a non-standard 1-ohm. When you replace it with a standard 4-ohm speaker, the stock amp can only drive it with a 1/4 normal power. It always cracks me up to hear people praise aftermarket subs, they are extremely muffled in the console because of the low power. It is true however, that you will never blow out an aftermarket sub at 1/4 power.
Either replace the speaker with the Quadratec replacement (also 1 ohm) or replace both sub and amp with aftermarket units at the same time.