One place to run coax is in your rear fender behind the tail light- you've already got a grommet there for the sunroof drain that is ripe for the disturbing if you swing back that direction, and plenty of room for drilling if not. But that gets the wires out of harm's way as far as the hatch and tail gate operation is concerned..
Are you installing just a 2m radio?
82 fj40, 99 uzj100, 06 gx470
05 525EXC, 01 XT225, 09 TTR125, 07 TTR90, 07 CRF50