Update
For those looking to use their factory crossbars with a Yakima box... First - to the guy who said his box was bouncing around - not sure how you achieved this - I'm guessing you overloaded it or did not have the clamps adjusted properly.
I just finished a roundtrip from New York to southwest virginia and back again. (8+ hours each way). Here are my oberservations:
1. The skybox 16 is a very good size for the T4R, I personally wouldn't get anything longer (81"). The 135 lb limit with the factory bars is actually about right once you load up the box.
2. When I first installed the box (empty) there was about 1/2" of clearance between the clamp bottoms and the roof (see other poster's excellent photos above). BUT - once you load the box up, the factory bars sag a little bit. In fact, I ended up putting 1"x1" squares of rubber between the clamps and the roof on the back bar because it was essentially sitting on the roof.
3. The box shimmied up and down very slightly at 75 MPH, but was very stable, made NO noise, stayed exactly where I put it on, and kept everything safe and dry (including in a driving thunderstorm).
4. WITH the box loaded with 100 lbs of stuff, drving 70 - 75 mph i consistently got 20.8 - 22.0 mpg.
5. Satellite radio - so here's the word.... The box overhanging the sharkfin DOES interfere SOME with reception. I'm not a satellite technician of course, but I know it works on line of sight for reception. The box essentialy blocks a certain percentage of sky from the antenna. On an open highway, there was no issue with reception. On a side road with tall trees close to the road, i got seom intermittant break-up of signal. And it was noticibly different without out the box - so - for a road trip, not really a big deal, driving around town, kinda, yes. I think getting some yakima crossbars will help b/c it will give some more space between the sharkfin and the box, hence more degrees of viewable sky.
6. The final word: I love the skybox16. Did exactly what i needed it to do, with minimal interference on my driving. With that said - I'm buying some yakima railgrabs and cross bars because the box does barely touch the rear spoiler when the tailgate is up (even if you adjust it as far forward as you can - it settles back once you drive.) I also don't like the box clamps touching the roof - hence the rubber foot pads. Not a big deal - but why should I put up with that? And finally, hopefully it will make for better satelite radio reception in close-in roads.
I would post pictures, but the previous poster who put up pics might as well of been looking at my truck. Those are a good reference.
Hope this helps anyone looking into the same setup as me.