Shoe manufacturers recommend replacing shoes every 500 or so miles. While this recommendation might be overly conservative, you normally need to retire your shoes long before they are showing obvious signs of cosmetic wear. Consider getting orthotics. For the vast majority of us who don't have perfect biomechanics, custom-made orthotics can correct or reduce improper motions which lead to chronic injuries. Allow for adequate recovery between tough workouts.
Tough workouts result in micro traumas to the muscles.
When these micro traumas are allowed to heal, the muscle is built up to a stronger state. Without adequate recovery, the muscle is continually broken down until an injury occurs. Ease into radically different changes to your training. Do a proper warm up and cool down. A proper warm up readies the muscles and connective tissues for the range of motion needed to do the workout - this should lessen the chances of muscle tears and pulls.