Reviving an old thread here, but in the case anyone else comes digging for ideas. This is long (sorry) but mostly pictures.
With aluminum rack options on the rise (
Prinsu Designs and
Sherpa Equipment Company type racks out there), I wanted to make something similar, but cheaper and not as apocalyptic-looking for my wife's 4Runner (she has this metric she made up called "lady-cool" and things that don't meet that requirement get veto'd). Don't get me wrong, both Prinsu and Sherpa make great products and I'm actually running slightly modified Sherpa racks on my Nissan Frontier. Our 4Runner gets less heavy use, but it's nice to be able to switch ski clamps, baskets, etc, or have a nice flat roof, WITHOUT needing special adapters for the factory rails. For a full aero bar setup from the likes of Yakima/Thule/Rhino Rack, you'll be into some big money pretty quickly, and still require some special adapters. Originally we went with a used Yakima rail-grab rack from craigslist (actually had it mounted on my wife's Jeep Liberty before we sold it and got the 4Runner).
So I ran a Yakima rail-grab system for a while with round bars. I liked this because of the simple snap-around clips that Yakima uses. They're super easy, convenient, and versatile. The negatives are the added height (not much, but still) once you get the bars, clamps, etc. I can barely fit out of the garage with a 1" lift and only running 32" tires with skis up there. Plus those dang Yakima round bars always rust out on the ends after a few seasons.
SO, I've been working on a cleaner system for my own, as well as a couple friend's 4Runners (only 4th gens so far, but probably 5th gens coming soon).
I used 80/20 extruded aluminum just like Prinsu/Sherpa use. Designed a few different types, but basically they're way more modular because you can drop carriage bolts or track nuts into the track and not have to buy the expensive aero bar clamps, etc.
This moves the weak point of the OEM rack from the crossbars to the feet where the OEM rails mount to the roof. I'm pretty comfortable with that, even for a larger/heavier load. At a fraction of the cost, I've done a pretty cool flush mount system that I'm super happy with. Check out a few pictures. You can barely see the from the ground/eye level, but they're there. Been messing around with both 1"x1" and 1"x2" bars. Both are pretty useful. They're completely aluminum and stainless steel, so no corrosion or rust. They're also low profile and unobtrusive (meets my wife's "lady-cool" criteria easily). The only downside is that they create a lot of wind noise since they are slotted aluminum. A fairing should help out a lot.
Sorry you have to see that Honda Ridgeline in the background. This was in someone else's garage.
Anyways, that's what I've come up with for mine. Let me know what you think.
Cheers.