I experienced what you are describing when I first quit. It's not unusual.
One thing that we KNOW is going on is that your lungs and bronchial tract are starting to clean themselves out for the first time in years. A lot of "stuff" is loosening up which can have the short term effect of making breathing a little harder.
I can't prove this, but I have a very strong suspicion that the cigarette companies put "bronchial dialators" in their product. These act like little mini ashma inhalers to open up breathing passageways with every puff to mask the true impact of smoking. If I'm right, then it will feel like it's harder to breath when you quit smoking (just want the tobacco companies want you to think: "Oh, smoking helps me breathe").
Of course, over the long haul, smoking kills you from inability to breathe, but for the short term ( a week or two), it may be something you have to work through.