The Rubicon doesn't hold enough for two on an extended outing, the ride is horrible, and there isn't that much room for passengers, yor planned uses outway any benefits fropm the F/R lockers. You can have dual ARB's in your '88 for under $2k(US). The '06 Runner is nice, a large interior, nice ride and a V8. This would make a good family rig, not a great off-roader do to its size, even teh right bumpers wont help that much. IMO, the last gen Runner really has gotten to big to be a good trail rig. The '99 Runner will work well for everything you want it to do, it will be comfy on long trips, hold 2 kids and gear for traveling, should last forever, and is of course quite bit more upscale than the '88 Runner. The FJC is nice but I didn't like driving one, I am 6'2" and even though there is plenty of headroom, do to the design it makes you feel like you have to duck down to see out the windows, and like the Jeep there isn't that much storage room.

If you have never owned(*my*) a new car before, I would buy the '06 Runner for family travel/outings, and keep the '88 Runner for the back woods camping trips, and equip it with lockers. This will give you the best of both and since the '88 is already paid for, off-road dents wont hurt as much, atleast not as much as denting a $40k rig.

However if you don't want to keep the '88, I would look into a late '90's Landcruiser. They come equipped with everything you are after, lockers, luxery, room, V8, and are still small enough to make a good trail rig out of, and you should be able to find one for less than the '06 Runner.