Hi,
One of the consequences of vigorous exercise—heavy weight lifting, a tough day of speed work on the track, or the stairclimber at the gym—is an accumulation of lactic acid in the muscles. Lactic acid is a normal byproduct of muscle metabolism, but it can irritate muscles and cause discomfort and soreness.
Take a hot shower for two minutes. Then turn on the cold and let it run full throttle for 30 seconds. Repeat the process five to ten times. As you switch from hot water to cold, your blood vessels actually open and close, flushing lactic acid--which causes muscle soreness--out of the muscles.
Over-the-counter anti-inflammatories such as Nuprin, Advil, Tylenol and Anacin-3--medications containing ibuprofen or acetaminophencan help calm inflammation and soreness.
Warm-up exercises before and stretches after your routine will help in reducing it.
ref:http://www.mothernature.com/Library/Bookshelf/Books/48/140.cfm
I got very sore ankles when I started jogging. It felt like I had glass in the joint. I ended up having to get the best running shoes I could afford from a specialist shop that videoed my running style etc.
I have since then been running for nearly a year now with few problems. I still get some pains if I run on uneven ground but if I stick to paved areas, no problems.
Good luck.