Dwarf,
See my post below, "New system installed." We are about to do the very same thing, softtop and p/u tailgate. We have the top, just looking for a decent tailgate. Along with the front speakers in the stock location, we added two 4" speakers in the center of the dash, and a couple of 5.25's in the kick panels and the 6x9's close behind the front seats, hopefully this won't change the sound much when the top comes off. We will experiment with with a sub once the softtop is installed.