That's a very nice writeup!!!
I put my bass gain control one one of the removable squares in the center console, put my amp in the driver side rear fender (similar to the sub but opposite side), ran my wires inside the car (through trim and rear seatbelt areas, following the main wire harness down the driver side and installed a manual circuit breaker near the battery (in case I ever want to enter in a competition).
Many ways to do a system! I rather like your amp rack Nibis. I may relocate mine and make something similar.