I've searched on this, but haven't found much definitive....is there anywhere else (such as beside the stock subs) that other subs could be put? Or are we pretty much relegated to a flat box in the trunk under the conv top bay? I realize mounting depth is a big problem with replacing the subs in back, and it not being an even semi-sealed box hurts that location as well....but has it been done?

It's a given that you have to separate-amp any subs beyond stock. After the door spears were capped and replaced and deck replaced, you can definitely hear when the stock amp runs out of juice and when those poor 6" subs run out of throw.