I concur with ace, the MY '06 stereo/headunit really isn't that bad, all things considered. After swapping out the headunit, I'm actually somewhat impressed with how decent the stereo sounded with the factory headunit, considering the majority of honda oem stereos are generally quite poor. That's not to say it's not worth replacing if you're particular about SQ, but I certainly wouldn't say it's poor, like many of the early models likely are..

To the OP, I'd say just buy a pair of woofers to replace the woofers in the doors now. My passenger side woofer as well sounds like it's blown, so I understand what you're saying. I wouldn't recommend a coax speaker as you'll be getting highs then from the woofer location AND from the tweeter in the doors that are separate. I'm sure you can find aftermarket replacement woofers if you like. I'd also just get a pair, so the left and right woofers match, otherwise it could sound a little strange.

 

Most factory "components" just have an inline resistor leading to the tweeter. I would be surprised if the S2000 were any different.