Welcome to the site!
Lets get the basics down first, the basics are key to being a "pro" reptile keeper!
Read through these threads, unfortunately many pet store employees aren't very knowledgable and give out bad advice. These threads will ensure that you know what you are doing.
Basic Care: http://ball-pythons.net/forums/showt...ius)-Caresheet
Cage Setup: http://ball-pythons.net/forums/showt...With-Pictures!
Cage Heating/Temperatures: http://ball-pythons.net/forums/showt...t-Thermometers
Ok, now that you have the basics down lets get to your questions.
There are a lot of possible causes of missing scales. For now I wouldn't be too worried about them, many times our snake will be good as new after a shed. If your BP is still missing scales after the shed then you might want to look into the cause, but for now there isn't much you can do, and it shouldn't be an issue to your BP.
Mites on the other hand are a big issue. To get rid of the mites here is what I would recommend:
1. remove everything from the snakes cage and clean it throughly. Spray the cage down with a mite killer ( I suggest prevent a mite http://lllreptile.com/store/catalog/...rovent-a-mite/) Follow the mite killers instruction to the letter, some of these chemicals are dangerous, and if used improperly bad things can happen.
2. Place a single of paper towels in the cage for substrate. No wood chips/reptile carpet, just paper towels. This will prevent mites from hiding in the substrate, and will make seeing the black bug easier.
3. Keep the cage as minimalistic as possible. You don't want to give the mites anywhere to hide or lay eggs.
Something lik this:
4. soak your snake 1-2 times a day in warm (not hot, water temp in the 80's F) with a drop of Dawn dish soap in it. This will help to remove the mites from the snake.
5. IN a week or so (whatever the mite spray directions say) repeat this process to ensure that the mites are gone.
If you have any questions feel free to ask.
A description of your setup would allow us to find any issues you may have.
1. What type/size cage
2. What you are using to heat the cage
3. What you are using to measure temperatures/humidity in the cage
4. Any thermostats/temperature controllers?
5. Current cage temperatures.humidity
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