Sandy,
Bike shops do not have much of a mark up on the bikes so in order to make money and survive, they need to charge enough on their products and their services. It would have been a nice good will gesture to have installed the computer for free ( and I DO think the price w/wo installation should be listed on the computer) but I don't think it's a common practice. It's a service - it takes time- they charge for it. As for switching out stem (or any other parts), you should only have been charged for the difference in cost between the two. Obviously, if you now have a better stem (or pedals, saddle) that costs more, they can't just give it away. So I wouldn't think too poorly of the bike shop. If it bothers you, mention to them that you didn't realize there would be an extra charge, and that you'd appreciate it, in the future, if they would be more clear about their charges.
Anyway, now that you have it, just enjoy that new bike! It sounds like a beauty!
annie
Time is a companion that goes with us on a journey. It reminds us to cherish each moment, because it will never come again. What we leave behind is not as important as how we have lived." Captain Jean Luc Picard