First don't get caught up in the megapixel race. If you put more pixel sites on a give size sensor, you will increase the noise of that sensor. Cameras like the 1Ds and MkII have larger sensor to go with their increased pixel count. The number of pixels result in higher resolution, but if the size of the pixels decrease in size, so they fit on a certain size chip, the accuracy of the information they record goes down, resulting in noise. So if the new "10D" increases the pixel count without increasing the chip size, the new chip will be noisier. The new 8mp cameras: Canon Pro 1, Minolta A2, Sony 828, etc, are somewhat hamstrung by noise.
I try to keep my camera turned off, pointed down, and caps on everything, until they're used, when changing lenses. I have had to blow dust off my sensor a few times since I bought the camera 6 months ago. I have had to use the copperhill method once to remove some stubborn dust, but generally a good blow with a Giottos Rocket does the trick. On a film camera you get a new "sensor" every frame you take, on a DSLR the same sensor takes all of the pictures, it's not surprizing it gets some dust on it. When you change lenses the mirror is exposed to the elements, and right under the mirror is the sensor, or film, it's no wonder that some dust gets in there. I have the Kinetronics Speck grabber but I am wary of using it on the sensor, I don't know what it uses for it's sticky, but I don't want to risk getting whatever it is on my sensor.
I personally prefer microfiber to clean my lenses, I try my best to keep my fingers off them so most of my cleaning is just a very light wiping with micro fiber or brushing with a lipstick brush. If I do have some kind of smudge, I use a small amout of lens cleaning fluid with my microfiber to carefully remove the smudges.
Your lens focuses with the lens wide open, your focus sensor needs a certain amount of light to be able to "see" the contrast to focus on. If 5.6 is wide open for your lens, it is just enough light to allow your auto focus to work properly. Any less light than that, such as a 2x tele coverter on a 5.6 lens and the auto focus just lacks the light needed to focus properly.