I have the same JBL system in my 97 EB. I am also trying to determine the best way to make improvements to it. The first improvement I am going to make is to upgrade all the door speakers. The factory "premium" speakers are anything but premium. They are basic paper cones with a "wizzer" cone (this is the cheapest speaker out there). The speaker is rated for more power than most wizzer type speakers, but there is only so much clarity you can get from a speaker like that. I am going to install some Pioneer 3 way 6x8's as soon as the budget allows.
As far as the rest of the system, it depends on how far you want to go. I like the factory stereo and CD changer, and I think that the subwoofer and amps are okay for the most part (I would like to get a little more bass from the system, but that might improve a little with the new door speakers). It gets complex and more expensive real quick when you start replacing amps or head units. It just depends on how much you want to spend!
Pacman