The shims have a slot in them that drops over the screw between the hinge and the A pillar it screws to. If you put one between the bottom hinge and the pillar, it will raise the bottom of the door at the back relative to the top of the door where you didn't put a shim. I have done this on my brother's old Bronco and it worked perfectly. The standard USA type shims are designed to slide down over the top and bottom screws that the USA hinges have. I can't remember if the FJ hinges have the screws the same distance apart as the Ford did, but if they are too far apart, you may need to use 2 shims. One for the top screw and one for the bottom screw.
Does this make things any clearer? If not, I'll take another stab at it...
Does this make things any clearer? If not, I'll take another stab at it...