I had a lightning prior to the cobra and had a great system in it which I recovered before selling. The head unit is a panasonic touch screen with an input for my ipod which contains my entire music library. I miss it. Also I heard its hard to get good bass response in a vert. The stock system sounds flat to me.
You can get excellent response with little effort and cost. Get a Kenwood sub amp for $129.00 and one 8" Rockford Fosgate sub in a box for $69 (I use a black bungee cord to hold sub box against rear seats, speaker pointed at the taillights;this allows me to move the sub at will) and you are ready to go! Connect to battery and one of the rear speakers and that's all you need to get decent bass at a low price.
The stock system should be enough to get what you need once you add a little low end.