I'm a Ham, I installed a mobile rig in my KJ about 2 years ago. I have a Yaesu FT-7800R with a faceplate separation kit, so I mounted the faceplate in the small cut-out space next to the cig-lighter (underneath the climate control panel). This space is really nice as it sits in the cut-out and isn't visible from the outside of the vehicle. I also have the mic attached to the faceplate display and it rests next to my 4X4 lever. I secured the radio base unit underneath the passenger seat with wire ties to the seat mount, running the faceplate wiring along the passenger side of the center console and then out under the seat.
For power, I initially wired it off of the cig-port but I wanted to run 50W tx power, so I drilled a hole through the firewall on the passenger side and ran the two wires directly to the battery terminals underneath the hood. As far as antennas go, I have a stealthy-looking NMO mount antenna which is mounted to the right-side of the tailgate. It is mounted so it clears the rear window when it opens, pretty much lined up with the radio antenna on the front for AM/FM. The coax wire for the antenna runs through the tailgate and skips over where the hinge is on the left side, and then I ran the wire inside the left-side panel in the trunk and then across the car underneath the rear seats, and finally underneath the passenger side door mounting in the back and finally back out under the passenger seat.
My next project is to install an external speaker or connect it directly to my stereo via my ipod kit, since the sound comes out of the base unit and is muffled coming from underneath the pax seat.
Wow, that description was complicated! I'll post pics if someone tells me how. I love the set-up though, it looks really stealthy so nobody can tell the radio is there, but I have access to a full mobile station for 2M and 70cm as well as scanning ability for pretty much everything.