You can add a bit of thump with just a good set of 4-way speakers doors/rear panels if your stock system is ok otherwise, and you want to keep it all.
If you try to replace the subwoofer in the stock sub box, be sure to compare measurements. Not sure there is a good source for that size sub, tho.
The OE system in my '90 anny wasn't working when I got the car in 2008, so... ended up removing the stock sub amp and woofer/box, then buying a scosche harness that replaces those so the main speaker circuit is bridged back there. Replaced the head unit with a Jensen 7" flip LCD (GPS, hand's free calling, DVD, 5.1 surround, USB/SD, etc. etc.) and replaced the CD player with an Alpine center speaker.
Added a fosgate sub amp that drives a pair of 10" boxed subs and the Alpine center, then replaced all four mains w/4-ways, then added a pair of tweeters that mount to the covers inside the mirrors on the doors. Topped it off w/an 8 farad cap w/volt & amp meters.
Info you might find handy here:
http://www.35thatr.org/Radio/RadioRelatedPages.htm