An increase of heart rate occurs because there are higher demands required achieve do the set activity. When physical activity is attempted the requirements of oxygen to the muscles are increased in order to shut down glycogen. Once glycogen is broken down ATP is produced, ATP releases energy that allows you to move. Since more oxygen is required for the muscles, more blood must be pumped through the body which results in an increase of waste. A higher heart rate effects performance in a negative way.
Breathing rate is another big short term effect because it can either minimize or maximize your performance the higher the breathing rate the worse the performance. During exercise the muscle cells use up more oxygen and produce increased amounts of carbon dioxide. Your lungs and heart have to work harder to supply the extra oxygen and remove the carbon dioxide. Your breathing rate increases and you breathe more deeply. Considering the anaerobic system is being used the body still needs to make up for the loss of oxygen in order to break down lactic acid and replenish energy supplies.
Skin colour is one of the most noticeable effects during exercise. Humans maintain a constant internal body temperature (homoethermic). To control the bodies temperature during or after exercise, the flow of blood is directed away from the core, to the skin where excess heat can escape. There are a lot of small capillaries in the face close to the skin, this is why your face turns more red than other areas. This is called vasodilation. Change in skin colour doesn't really affect performance.
Perspiration plays a big role in cooling you down after exercise, As body temperature increases, sweat production increases. When your blood temperature becomes too high, vasodilation causes the flow of sweat which releases excess heat out into the environment and also onto your skin which will then evaporate to cool you down. This is why your perspiration levels increase during exercise.
Muscle soreness is one of the most negative short term effects of exercise, when muscles are working waste products are produced when producing energy. One of them is lactic acid, lactic acid consists of muscle tightness and fatigue. This can be removed by warming down/stretching. These can affect performance greatly as the body wont be moving as well as it did before.
Question 2: How/why is the major is the major energy system used in and how/why does that effect the way you run?
The main energy system is ATP, It is composed of three phosphate groups. The energy that is stored within an ATP molecule is released for your muscles to use when the bond between the second and third phosphate groups is broken. Breaking this bond releases the third phosphate group on its own and reduces the ATP molecule to ADP. The ADP molecule can be restored back to its ATP form by refilling the missing phosphate group. This is the main energy system because it controls the intensity, the duration and the waste products of your body. This affects the duration and intensity of which you run at.