If you just want two load bars, and attach a tray to that, you can easily install something like Yakima Side Loader brackets later. On my '05 Chevy RB, I installed roof tracks the entire length of the penthouse so I can place load bars at any location, and I think they look much better than brackets hanging off the side. When you pop the load bars off, the top looks very clean and there is no wind resistance. I installed Yakima tracks, but I understand they are identical to Thule's.
The thing is, installing them was not as straight-forward as I thought it was going to be. That's because I needed to install them with the bolts extending down inside the canvas area, rather than outside as some have been able to do: See http://sportsmobileforum.com/viewtopic. ... highlight=
Perhaps there's a difference in width between Chevy and Ford penthouses. It worked fine, but I needed to remove the curtains (not difficult) and make sure the bolts wouldn't run into existing hardware. I had to purchase 2" bolts, use large fender washers, and make sure the installation was water proof. Perhaps the hardest part was cutting the bolts off flush after installation so the curtains would go on okay and not risk the bolts puncturing a hole in something. In other words, if you want full-length tracks installed and you want to save yourself a fair amount of time and effort, consider having the shop do it for you.
I also recently installed an Alluminess ladder. Its not hard to do, and it looks and works great. Though I did opt to purchase and use larger bolts for mounting the bottom plate to the van.
If you plan to carry much weight up there, get the electric lift. I can lift two 18' sea kayaks with my manual top (with springs shortened two links), but just barely. If you're going to keep a rack on all the time, you'll probably want to adjust your springs accordingly, and you can have SMB do that if they're installing the rack.