My Achilles tendon hurts?

Well, you could have injured the tendon, and only a physician can do the exams and determine if that has happened. I would start there, just to make sure that you are not making it worse by stretching and running. Once you have the all clear, you have already seen that you do need to properly warm up before exercising. Get a book or video on warm ups and learn to do it carefully and slowly, and don't exercise without carefully warming up. A better option for exercising for you may be to join a gym, get a personal trainer to show you how to use the machines, and stay away from exercises that irritate your foot and ankle (like treadmill or elliptical machines). There are plenty of other machines in gyms that will exercise your body without injuring it. It is best to seek professional help, as it is very easy to injure yourself in or outside the gym without someone who understands body mechanics and anatomy to explain to you how to do the workouts.