Originally Answered: Yoga Questions?
1. Provided that there is no pain associated with your joints cracking, this is nothing to worry about. It's not something you need to try to make happen, but it's not a bad thing either.
When you perform yoga asanas (poses), your joints may crack for a couple of reasons:
i.) Your joints are lubricated by a fluid known as sinovial fluid. This fluid is found in the joint capsules which surround the cartilage surfaces where your bones meet. When you perform asanas, you cause small changes in pressure within the joint capsules. These pressure changes may cause gasses which are normally dissolved in the sinovial fluid to "pop" out of solution, causing the sound that you hear. Once the joint is returned to a resting state, the pressure inside the joint capsule will normalize and these gases will dissolve back into the sinovial fluid. 
ii.) Your muscles are attached to your bones by tough bands of connective tissue known as tendons. Tendons must cross at least one joint in order to cause motion and, when that joint moves, the tendon's position with respect to the joint changes. When you perform asanas, your tendons will shift slightly and sometimes snap back to their original position suddenly -- again causing that popping or cracking noise. 
These are normal processes and the sounds are neither good nor bad, just a part of the process.
2. If you have pain associated with the position, you should stop. Yoga poses should never be painful. If there is no pain, whether or not to continue will depend on the type of pose you are doing.
If you are doing an intense strength-training pose such as a warrior pose ( http://yogajournal.com/poses/495 ) some shaking of the muscles which are doing that strengthening work is normal. This happens because you are asking your muscles to work harder than they are accustomed to doing and your muscles are growing fatigued. This is not a bad thing. 
Strength training works by "overworking" your muscles. You ask your muscles for more than they are currently able to handle. This creates microscopic tears in your muscles. Over the next couple of days, while you are resting, your muscles will repair themselves, and that new, repaired muscle tissue will be stronger. 
If you are shaking during poses which are meant to be gentle stretching poses, such as any of the forward folding poses ( http://yogajournal.com/poses/476 ) you should back off. You don't necessarily need to stop doing the pose. Just ease off on it a little.
When we stretch, we want our muscles to be relaxed in order to achieve maximum flexibility benefits. Twitching muscles during a stretch indicate that you are pushing too hard. Your muscles are fighting the stretch and can clench up. This decreases the effectiveness of the stretch and can potentially lead to injury. 
3. A number of different theories have been proposed for why athletes experience muscle cramping during exercise. Recent studies suggest that the most likely cause of these cramps is a malfunctioning of the communication system between our muscles and our central nervous system.  This malfunctioning is thought to be related to poor posture, inefficient biomechanics and other factors related to poor flexibility. 
Since yoga is such a wonderful exercise for helping you to increase your flexibility, it should therefore be effective in helping to reduce your experience of muscle cramping during running. Additionally, studies have shown that an effective stretching routine during warm-up and cool-down periods for running and other physical exercises can help to prevent cramping. 
4. Yes. Yoga will help you get into better shape. An effectively sequenced practice of yoga poses will strengthen and tone your whole body. In particular, scientific studies of the effects of regular yoga practice on physical fitness have concluded that yoga can help you increase:
i. muscular strength 
ii. muscular endurance 
iii. flexibility 
iv. lung capacity 
v. cardio-respiratory efficiency 
5. Everybody is different. Some people will experience noticeable improvements in their flexibility after only a couple of weeks. For others, it may take a few months.
A participant in one study, which involved 4 sessions of yoga per week, each 1 hour and 25 minutes in duration, for a period of eight weeks, experienced a 188% increase in flexibility over the course of the eight weeks! 
There is no guarantee that you will experience that degree of improvement in so short a time period, but since you are young, are practicing yoga every day, and are new to flexibility training, my guess is that you will start to notice some improvements very quickly. (Please remember, however, that yoga is not a race. Yoga is designed to be practiced throughout our lives -- and one of the things it tries to teach us is patience!)