Here we have just about all of the wires in place and neatly labeled in case I have to open this thing up and do more work in the future. The trickiest one was the XBox360 Home/Guide button, but I tracked that thing down by trial and error and plugged it in too. What I did was to plug the joystick into my Windows XP VM (VMware Fusion FTW!), open up the control panel > game controllers and look at the buttons on screen. Then I screwed down the Home button wire to the ChimpSMD board. Then I took the other end of this wire and plugged it into one metal connector at a time of the other wiring harnesses connected to the MadCatz PCB and pressed the Home button. When I saw button 13 light up on my VM screen, I knew that I had found the right connection.
One other note I should add... It was a piece of cake to find what the wiring harness connections were for the first wiring harness connected to the Remora board. They're clearly labelled as "Ground, X, Y, A, B". But the rest of the buttons were not so easy. What I ended up doing was using a multimeter tester, set to test for continuity, and while holding one end to the loose wire, touch the other end of the multimeter prong to each of the quick disconnects on the Seimitsu buttons. When I heard a beep, that means I found which button corresponds to that wire.