A 12” in the trunk with ample power is plenty for almost everyone. My setup is a lot more compact than yours and most people can’t handle it for long.
Why did they not want the 6.5s on 2 channels and the mids/tweets on the other 2 with crossovers?
I mixed brands and the Rockford tech support knew more about my Alpine amp than Alpine did.
I had the 6 speaker system in my f150 and I used Forscan to change it to preamp level, tapped into the speaker wiring using plug adapters and added amps, better speakers and subs. It was pretty simple.
A Mustang is basically the same
For wiring I followed the instructions at the top of the page.
I made my own enclosure using the carpet from a wreck as the base. I have a pictorial thread on the process posted here somewhere.
I can't help you with either question but I ditched the 9 speaker system. Kept the head unit and added an Alpine R series amp, R series speakers and a RF Punch 12" sub. I spend under $1k and it is impressive!
I don't remember which one I used but it plugged right into the factory harness. If that is the one recommended then it is the one I used too because I got all my info from this group and it went very smoothly.