1 - Front door and rear deck are both 6 x 8, and the subs in the door are shallow mount 8". You will need to do some trimming or bending of a plastic piece to get aftermarket 8's in.
2, 3 and 5 - You can use a new amp in addition to the amp that comes with the shaker 500, but you will need the PAC Ford radio replacement unit to do so. It's all in how you connect it to the head unit. Goes like this, head unit to PAC to factory amp to new speakers. For the subs in the trunk, if you have the RCA jacks in the back of your head unit, just hook the aftermarket amp up to the head unit to power JUST your subs.
No idea about question 4.