I agree with the others -- start with replacing the saddle on your current bike. My best advice on saddles is to find a bike shop that will let you try out different saddles or allows exchanges if you buy one that is not comfortable. They might also be able to tell if it's just a matter of adjustment. Many people find saddles uncomfortable because they have them positioned wrong -- too low or high, tilted rather than level, too far forward or back.

Bullhorns or handlebar extensions are good options if you don't want drop bars, allowing you more positions for comfort and aerodynamics than plain old flatbars. Most of the issues with commuting you will work out by just doing it. The important thing is to take the first step, or pedal stroke.