1. No, not easily. But I suppose you could always use a small aftermarket amp to power the factory sub.
If you can still get the factory radio back, better to put it back in place----the four factory speakers sound terrible by themselves. The loss of the sub, the amp, the changer, and the rear seat controls.....it just wouldn't be worth it to me to go through all that just to have a CD slot in the dash. Plus, the factory unit looks and fits better, and is easier to use.
On the other hand, if your budget allows, you could keep the radio you have, but buy an Eclipse changer to go with it, a subwoofer, box, and amp, a 4-channel amp for the main speakers, and one of those PAC interfaces to keep the rear seat controls.