I think there was a post here about this topic a few weeks ago.
To install the rails as they do in the factory is a PITA. A clever guy, however, recently found that when you don't screw the existing end cap screws all the way in, leaving just enough that the cap will slide between the screw head and body with a bit of friction, it works out well. That and the rail screws clamping everything down is enough to hold the end caps in place, which are not load bearing anyway. There is no need to drill.
Once the end caps are slid into place and onto the ends of the rails, the rails can be tighten down with the provided hardware and everything is held securely in place. No fuss, about 30 minutes to an hour job. You may have to do this kind of thing yourself as it is not per Jeeps official instruction, although you may find an independent shop willing. Oh... some say to put some silicon around the screw holes to prevent leaks.
About post 61 of this thread contains photos:
***** = j e e p g a r a g e