Having owned both, I would suggest a Tracker for a daily driver over that kind of distance.
The ride in a Samurai is best described as "harsh" on the type of roads that you described. I drove a Sammi to work for several years when I lived in the Chicago suburbs. I had no problem keeping warm, even in subzero temps, as long as the engine was running. when you shut it down, the interior cooled down very quickly. The most annoying thing was every time a truck went by going the other way on a two lane, the velcro on the top would rip loose.
The ride in a Tracker is a bit more civilized, the top is a better design, and the fuel consumption is comparable (25 mpg for the Sammi and 27 for the Tracker (on road in 2wd)). The fuel injected engine is easier to start in extreme cold. While the Sammi is awesome off-road, a stock Tracker is also very capable. I would recommend a '96 or newer Tracker/Sidekick with a 16 valve engine and a 5 speed.