All the speakers should still be 6x8's all around. As far as subs do you want to replace the 8"s in the doors or are you looking to add an aftermarket sub?
Yes Ford uses 6x8's not 6x9's. As far as a sub I dont think there is anything that is a direct plug in. Your going to have to get a signal from the rear speakers and run a power wire for the amplifier from your battery.