I've got a rocking system in my '97 XLT. I believe all 4 door speakers were 6x8's. I got some Infinity ones off of eBay that have 100W peak power rating. Even without the subs, the system rocks hard compared to the factory system. Changing out the head unit is very simple, although if you have a CD changer in the center console, you will lose that feature. I don't believe there is any adapter to make the factory CD changer work with an aftermarket head unit, but I may be wrong about that.
For the subs, getting a sealed or ported box and putting it in the cargo area is by far your best choice. You won't have very much clearance under the rear seats, which will limit which subs you can get (you'd have to get low-profile subs). I have two 12" subs in a ported box with a 1920 watt amp attached to it and a 1.5 farad capacitor in parallel. My biggest problem has not been getting good sound out of it, but trying to vibration-proof the explorer because the subs vibrate the bejesus out of the truck!
The biggest problem with getting a full system set up is choosing a nice balance between cost and quality. But usually if you do your research well, you can get a great system for not a whole lot of money, which works out really well if you are an audophile like myself.
Let me know if you'd like more detailed specs about what I've installed, and what other people I know have installed. I did all the work myself, including putting dynamat on all the doors, so I can give you some tips and advice.