i would personally just pull the whole stock system out and start fresh. imo it will be easier this way.
for speakers in the back, i personally prefer the sound of components, but if you choose this route you are going to have to find a place to mount the tweeters.
if you dont want to do that just stick with 6x9s. also i've never heard of 6x9s wth tweeters in component form, unless you talking about 2way and 3way 6x9s in which case its just a coaxial setup with the tweeter (or midbass and tweeter in the case of a 3way) mounted infront of the woofer.
I would list the whole thing together, but also say that you will sell them individually. That way im sure something will sell.
What headunit do you plan on using?