Kizashi Club

I just recently got my kizashi but I was wondering if i could replace the 8 inch sub in the rear deck with one that is more powerful and sounds better?

So long as it's open air, you're not going to do much better. Money/time would be better spent on building a box around it.

The stories of how the system is wired leads me to believe there is serious room for improvement in the wiring and amp replacement.

Getting a better sub would only make it sound marginally better because of the open air around it, and it's still be powered by the stock amp.