Look up FJ Freedom Windows. They have them as a kit. I think I saw somewhere else that had them for a little cheaper too.Low tech but nice to have would be for the rear windows to vent open and the front seats to fold forward for easier rear access, both similar to the xtra cab pu's.
Also, the skid plate design leaves much to be desired, needs support out to the ends and could be tucked tighter. Mine folded on a rock and I've seen another thread where it acted as a mud scoop.