Gary,
I am really curious as to how the Yakima box was secured to the roof. Did you use a rack? Which rack and how was the rack secured through the roof? How far did the box over hang the door? I've got the same problem with space.
We put two truck-bed bike mounts (from performance.com)and secured them to the ladder tube-frame and steps with stainless U-bolts covered with rubber tubing. I will send a picture if you wish. So 2 bikes (or 1 bike and a tandem) mount vertically to the ladder secured by their front forks and a couple of bungees. Been out to Nova Scotia and back with bikes there. They stay a bit cleaner than a low-mount hitch rack. 26" front wheels bungee nicely inside the ladder frame (skewers removed)
Still have problems with skis (alpines fit under the bed/sofa) and boots etc. We also have a dog we renamed Visa - she's everywhere we want to be!
Cheers,
Ciaran.