Mine is a base coupe so there was no stock amp...

However, I did bypass the stock wiring. Ran two sets of RCA cables to the trunk where my amp is: one for the door speakers, one for the sub. Then ran two sets of speaker wire from the amp back up to the cross overs, mounted behind the kick panels. Then ran speaker wire into the door and to the tweeter and mid-woofer.

If I understand what you are trying to do, I think you can just buy a new head unit and use the internal amp on the head unit to push the stock speakers using the stock wiring.... not real sure about the stock tweeters though, b/c they may take less power than the internal amp puts out on your head unit.

For instance, my tweeters only take 20 watts rms and my head unit supposedly puts out 40. My amp puts out 75, but my crossovers that came with my door speakers splits the signal. Also not sure if the stock speakers have a crossover.

Hope that helps