Big question, are you planning on an off-road rig or more expedition style?
+1 to the mirrors, +1 to the rear diff breather, just did this as well. For the price and simplicity it's a quick improvement. As far as the rear lower control arms, I haven't had any problems with mine, and they have lots of battle scars on them, once again, depends on how you plan on using the vehicle.
My FJ came with a 3"OME lift and 33" tires, and ARB roof rack already, so my first real mod was rock sliders, they saved the rig from some serious damage early on. I used the factory skid plates for a couple runs until they were bent beyond repair, and then replaced with a Ricochet HD aluminum skid set. I haven't hit anything that they couldn't handle yet.
I love the OME lift for the smooth ride, but I have always had it so can't compare to stock. My ARB roof rack is great, but I am thinking about replacing it/modifying now that I am thinking about a RTT. I would probably go with a low profile style like a Baja rack expedition or utility if I had to buy a new one.
and as
@ASNOBODY said, the Blue Room is a great wealth of info/pics/and vids for FJs