Tourists typically position bars higher than roadies because they spend much more time in the saddle, day after day, with little "need for speed", and they are not under so much peer pressure to conform to others' ideas of what is right. IOW, comfort takes top priority. LBS mechanics frequently set bars way too low and cut steerer too short because they only know how to build road bikes.
Obviously the problem is if you cut the steerer too short it limits your bar height. It is possible to go with a very steep (35d) stem afterwards to maximize height, but it's better to not cut the steerer tube too short in the first place. Starting with a horizontal or inverted stem will allow you to retain maximum steerer tube length until you determine final configuration. It is not unusual for bicyclists to experiment with two or more stems when setting up a new bike, particularly in the case of one lacking recent bicycling experience. Many people building a bike use their last bike as a starting template, which can be good or bad.
I would start with the bar 2-5 cm above saddle height. It's OK to leave 5 cm or more of steerer tube above stem until you determine best fit, it does look odd but who cares. Be sure to put spacers and a cap on the tube above stem, as the sharp edge of steering tube could injure you otherwise.
You don't need a special tool to install a star nut. You can actually use anything to bang it into a steel steerer tube, even a long bolt that fits the star nut threads with a couple nuts jammed together 1 cm from end (homemade star nut tool) will suffice. Pipe cutters make an excellent steering tube cutter too, but it is necessary to file some afterwards because the cutter wheel will expand the diameter slightly as it cuts through the wall.
The "stack height" of stems varies from one type stem to next, there is no standard, but most all are 37-45mm, or ~40mm.
Last edited by seeker333; 04-19-13 at 10:13 AM.