Rack update - I don't know if this was strictly necessary, but it irked me not to have a stouter roof platform than stock. Also a longer one. The stock configuration throws away a lot of length and a little bit of width.
LFD Off road has a pretty cool system in which you can buy their ruggedized cross bars which will fit the stock rails and then buy their longer and stouter rails and put the same cross bars on those rails. I didn't do it that way, but buying only the side rails and 4 cross bars saved me quite a bit of money over a full rack which I didn't need. Both the side rails and cross bars have lots of slots and holes in them to rig things up to your liking without drilling any holes.
I bolted some hi-lift brand hi-lift mounts to the side rails. It's a location I've used a lot and like. On the other side, I have maxtrax with shovel on top and a 2.5 gallon gas rotopax directly behind it. Either location will take more on top - a second set of maxtrax or a second 2.5 rotopax. That leaves me a good 2 feet of width or more for the entire length of the rack for lumber or what have you.
The big problem I had to overcome was horrendous wind noise. The little fairing I got from LFD was worthless as a fairing, but a great hard location to mount a real fairing. I had put some stuff on top of Kevin's Xterra and was worried about wind noise. He didn't have any wind noise at all -- but the Xterra has a nice fairing built in that comes all the way off of the roof to the top of the rack. I took note of that and decided to create the same thing. I went down to Barney Brother's Off Road and went "shopping" in their bone yard for a likely looking piece of plastic. I ended up with a genuine toyota branded part. It looks like it may have been the factory plastic skid plate from the front of a Tundra. Heck, it might have come off of Scot's Tundra. It was already nicey contoured and looked sort of like a fairing. I trimmed it to match the roof curvature on the 4runner, shortened the top and trimmed the sides. Then I bolted it to the metal fairing from LFD. I really think there is less wind noise now with all that stuff up there than there was with an empty factory roof rack and there has been no change in gas mileage. The only time there is wind noise now is in a *heavy* cross wind.