Final Results
It took about 4 weeks to complete and I'm pretty happy with the results. It's a modular system which is what I wanted. I still have access to my spare and I can still put long things into my car by removing the sub.
The sound dampening works pretty well. Before, I could hear my motor at 4000 rpm with my music at a medium volume. Now I cant hear the motor at all with medium music. The road noise by the tires has decreased. Highway driving is more quiet. I highly recommend sound dampening the cabin if you own a Honda. It's well worth the time and the small materials investment.
The sub is a JL Audio 12W6V2. One amp is a Hifonics ZX6000 for the sub. It puts out 600Wx1 at 4 ohms. The other amp is a Hifonics ZX6400 for the 4 speakers. It puts out 85Wx4 at 4 ohms.
This is the Kenwood hideaway box under the drivers seat.

Here's pictures from the outside.




The sub and rack mount just far enough back so my trap door still opens.

Pictures from the inside.



Here's the sub unhooked and hooked up with custom brackets.


This is where I mounted the remote boost control boxes for the amps.

Page 1: My Car
Page 2: Original System
Page 3: New Trunk Floor
Page 4: Sound Deadening the Trunk
Page 5: Sound Deadening the Doors
Page 6: Sound Deadening the Cabin
Page 7: Sub Box and Amp Rack
Page 8: Installation
Page 9: Finished Result
Page 10: Updated Finished Results