Ok I only read the first post I am short on time.. Are you sure its a "good hurt" vs a "bad hurt" after your 3 mile ride? If your bike isn't adjusted right / right size for you, you could be getting bad hurt. Bad hurt usually effects joints like the knees, ankles, shoulder, elbows and tendons where the muscle attaches to your skeletal structure. What I call "bad hurt" represents damage to your body that can become permanent or reoccuring soreness.

Your body should adapt to the stress after a short time and a month seems pretty long but it can take a while. "Good hurt" is called DOMS by weight lifters and health professionals and stands for Delayed Onset Muscle Soreness. It represents your muscles breaking down and regrowing stronger. When I took a weight lifting class at college the general feeling was although annoying, DOMS is fine because it ties in to a reaction of your body getting stronger (kind of like how a suntan is supposed to help prevent the sun from hurting you, your body adapts). I found an article on it and it says massaging can reduce the pain by %30:

http://sportsmedicine.about.com/cs/injuries/a/doms.htm