In my case, I just did away with the stock speaker placemente. I work in audio, and the stock placement is actually the worse possible place to put speakers as far as sound quality goes. I decided to use modpods instead located under the doors (with 5.25" round speakers), and they were MUUUUUUUUCH easier to do than trying to uninstall and re-install the stock speakers. I used sound wedges between the roll cage and the wheel well for the rear speakers with 9X6 speakers. All 4 speakers are 4-way speakers with HDLD (high Density Layered Diaphragm, made from polypropylene, so it will resist water and sun a little better than other speakers).
Granted, as far a security goes, these speakers are out in the open view (without even getting into the fact that the interior of my jeep is all black, but the speakers are RED and the grill is SILVER, so you can see these suckers from a mile away!). But that is way I typically ride with a hard top anyway... When I go offroading, I plan to take out the subwoofer unit in the back and the amp under the driver seat (you only need to remove one screw and the cable connections to do this), so they wont be damaged (and so they dont take up all that space!), and put on the soft top.
In any case, this is another option...
Felipe