Not sure how your amp is doing on the back of that box, but same car, similar setup and had my amp on the top of the box ... because I didn't have anything boosting it up, like washer's between the plate, it more-less arched itself out due to the heavy vibrations.
To avoid this, the amp was moved to the back of the box, vertically.
Just throwing that out there ... I see the amp on top and I get worried now lol
Oh and the trunk is rising huh ... friggin' cars, mine was beginning to do that too ... if it rain, small leak in the back (for me) ...