The shift knob unscrews from the shaft, so that's no big deal. A few companies make shift knobs that are sort of adjustable height, so that might help you out--don't get one that has a "universal attachment", make sure it's a threaded shaft. I forget what the threading is, but all mazda manauls. are the same.
For a shift boot, go to redlinegoods.com. They have tons of colors and styles and can be ordered in custom heights for short shifters as well. They aren't expensive either!