Don't run it through the body, keep it on the frame. The movement between the body and frame could eventually crack the line. I'm pretty sure that's why the factory made a few coils in the lines where they mate up with the master cylinder, to allow them to flex and absorb vibration. A quick look under a car at a junk yard will tell you how the factory did it, but you don't have to do it the same way if you don't want to.
I would just run it along the driver's frame rail, from the proportioning valve back to where the rear brake hose connects to the frame, which is just inboard of where the drivers side upper trailing arm bolts to the frame. If this doesn't make sense let me know, I'll try to take a couple pics.