The Ford Shaker stuff is fairly unique in design. To replace any aspect of it means that you pretty much need to go aftermarket for all of it. What are your goals for the sound system anyways? Better tonality? Louder sound? The current one should already be able to achieve SPLs in the cabin of around 105 - 110 dB. Prolonged exposure to sound above 90 dB causes permanent hearing damage. Exposure to 120 dB + causes immediate and permanent damage. Is there a specific aspect of the current system that you don’t like? Once you define your goals then you can start getting into the specifics of achieving it and selecting gear. After you’ve developed a concept for what gear you want then practical issues can start to be figured out, component location, wiring, etc.
I am a HARD bass fan although I like to hear the mid and high notes while my doors are nearly falling off. I love my music loud, but can't seem to turn it high enough to meet my satisfaction without hearing them clip.