This is coming from my running experience, which includes triathlons since 1983, road racing, and cross country teams in high school and college.
The main things you want to worry about are the core muscles and the major muscle groups of the lower body, which include the hamstrings (back of leg), quadriceps (front of leg), gluteal muscles (butt), abdominals, lower back and calves/foot flexors (lower leg muscles).
This is a stretching routine that takes me about 15-20 minutes to do, you make take a bit longer until you get used to the different stretches. Each stretch should be held for ~ 20 seconds, then relax a bit and then stretch slightly further for another 20-30 seconds.
- Hamstring - Stand with feet together, legs very slightly bent. Lean forward at the waist, keeping back straight and reach towards floor with fingers.
- Hamstring/groin - Same as # 1, but put your feet slightly wider than shoulder width, toes pointing forward and not out.
- Quadriceps - Stand next to a support, pick foot up behind you. Grab ankle, and pull towards butt. NOTE: This can place some stress on the knees, so if you have knee problems I would recommend an alternate quad stretch. Also, try to keep the tension in line with the leg, do not pull to one side or the other.
- Groin - Butterfly - Sit down, place soles of feet together. Draw feet close to crotch, grab ankles and place elbows across mid thigh. Press down gently until you feel stretch. The closer your feet are, the more the stretch.
- Lower back/hamstring - Hurdler - Sit with one foot extended, the sole of your other foot against the thigh of the out leg. Lean forward over leg, then after that stretch, turn and lean out over bent leg. Switch legs and repeat.
- Lower back/abs - sitting, place sole of foot against butt (So for left leg, place it against the bottom part of your right butt). Place other foot over your leg, with your foot flat on floor, outside of bent knee. Take your opposite arm (So in this example, right knee is up, use left arm) and place upper arm on outside of knee. Gently push and try to look behind you. Switch and repeat.
- Lower back/abs - If the above is too hard, lay flat. Stick one leg straight up towards ceiling, then try to touch it to ground at hip level on opposite side of body. Keep hips as flat as possible.
- Abs/shins - Roll on to stomach. Place hands by shoulders/ribs (Like a close pushup), then push upper body up. Keep hips/legs flat on floor. Feet should be flat (Tops of feet on floor) as possible.
- Lower back - Keeping feet/lower legs flat on floor, sit back on heels, then "ball up" and hug your knees, forehead on floor (You should look kinda like an egg)
- Calves - Put feet flat on floor, and get in a bent/piked pushup type position. Walk your hands forward until you can just barely keep your heels on the floor, knees slightly bent. Stretch with both feet on floor, then one foot on floor, then the other foot.
With any stretching routine, pay close attention to how you feel. You should feel some tension, but try to relax as much as possible. ANY pain, ANYWHERE, STOP! You are either very tight, or doing the stretch wrong, and in either case to keep stretching can do some serious damage. If you have any question, google "hamstring stretches" or similar, and look at the pictures.
If you would like a good reference book, "Stretching scientifically" is a good read, and there are quite a few good video references on youTube.