How do I change a road bike into a commuter bike? I have a road bike that I commute to work on, just a 9km trip each way.  I also have some tightness in my lower back, especially since I usually sit in front of a computer screen.  My wife wants me to change my road bike set up so that I am no longer bent over when riding, but have a more upright posture.  Can I change the stem and handle bars easily (and cheaply) for a flat bar configuration so as to turn my road bike into a commuter bike?

P.S. I am also planning on getting some panniers fitted, so as to take the weight of a backpack off me, but that will probably be another question.
You can probably change the stem to something shorter with more rise and not have anything else to change. This may be enough to relieve the back pressure and the drop bars will give you more hand positions which I've always found easier on my carpal tunnel.

Changing the handle bars to flat bars will mean you have to get a set of shifters and brake levers to go with the new handle bar style.

I'd also recommend that you get a set of full wrap fenders so you can keep the road spray to a minimum.

I'm a designer and programmer so I understand the issues around sitting all day. A better investment may be in your chair at the office and your desk. You're spending way more time sitting there every day than you are on your bike. That is the place that you can most likely get the most benefit by setting it up for a proper ergonomic workspace.