You can put your new head unit in this vette with a kit from Metra part # 99-3051. I can get it for you shipped for $20. drop me a pm if you need the kit. As for the speakers and output from the deck, the 50x4 is max output, just as psykod said. You can certainly use the deck to power your new speakers, but you may not hear them much with the targa top off... so you may want to consider adding an amp to your setup. The amp will allow you to turn up the volume without your new speakers getting all distorted sounding. You will of course be able to listen to them at a louder, and more clear level with an amp.
Up front, the speaker pod in the kickpanel is a 4" component setup in the bose pods under the carpet. The rears usually are a 6.5" speaker, but with the removal of the Bose pod, you can put in a 6x9. As for the sub box, a good installer, or stereo shop can custom build you a sub box to suit your needs based on the subwoofer and cargo space you are using for this box.
Good luck, and hope this helps!!