I did Black bear in 1997 or 98 in a Pathfinder MT. Having a MT vs AT will affect your approach to the steps. In an MT, the Pathfinder was about a 1:27 or so ratio vs 1:42 in Lo range for the FJ MT and probably 1:33 with the FJ AT. Rolling down in 4 Lo in the Pathfinder was not practical as the speed was too high and there was too much slipping on the rocks (it had rained 1/2 hour ago). Hence I rode the brakes and took one step down at a time (1st Lo, clutch in). In the FJ MT, it may be the same problem, unless you can tolerate the higher speeds and seeming lack of control! The sound of the creek nearby makes you not hear the slipping of the wheels so higher speeds seems scary. Although.... some people claim they regularly go down in 4 Lo, no problem, minimal brakes. I wouldn't advise overconfidence though.
FJ AT would be easier as you can apply the brakes to assist (without constantly de-clutching as in an MT, requiring another thing to deal with!)
With an MT and the pathfinder, the gradient+4Lo would overcome the power of the brakes, a scary sensation, the first time you experience it. I'm sure that wont be the case in an AT, so a little more relaxing, and easier to keep an eye on the road and glance at the beautiful views.
All of these trails, require only good All-terrain tires (not all season, MT is overkill). This and good brakes is probably more important than clearance and gearing in most SUV's (Even a stock FJ is overkill IMO) for all the passes here in the San Juan's (except Poughkeepsie Gulch).
One thing I've noticed is that when you sense a tipping over, its better to let off the brakes, roll through and then brake when the wheels are down. Its a little counter-intuitive. It always better to pick a more level path.
In the Pathfinder, it had a tighter turning radius than the FJ, and I took the first switchback after the steps in one go, i.e. went wide and then did a 3 point turn (right rear in the air!) as I went down to the waterfall. I'm sure I would have tipped over if I braked when the wheel was in the air.
I haven't been to the San Juans in my FJ.