The shaker 1000 is the shaker 500 with an additional sub in the trunk. Put simply you cannot re-use the shaker 1000 subwoofer box in the trunk. You will have to buy an aftermarket subwoofer/box/amplifier. TO reuse the shaker 500 8" door subs, only shelby makes subs that re-use the existing wires (you do have to cut some wires though) and the price is cheap at $130. However, unless you want the shakers to fall to pieces with a new headunit, you need to put polyfill in the subwoofer air space. To replace the door speakers, it's fairly simple and any 6x8 or 5x7 will work. To replace the rear speakers, that is fairly difficult on a 2008 mustang, but it also takes 5x7.
On an after-market head unit it requires two five volt regulators on the "remote-wire" that goes to the factory amps (two regulators since you have two factory amps). You can buy the expensive pac wiring harness that has it built-in though. On the metro install kit, you will have to cut some parts out.
maybe some pictures will help. click on the pictures for notes! Shaker 500 pictures by alwaysonjohn - Photobucket