Samantha,
It sounds like your shoes could be your problem with your running pain. Just like having a bike fitted properly you running and cycling shoes make a big difference in your enjoyment. Stick with your plans, fitness and health will come with your efforts. Regardless of your current weight level, the Clydesdale and Athena Forum is a good place to interact with cyclist that are working towards weight loss goals and maintenance. Don't let the weights stated for men and women, those are arbitrary and used for some weight handicapping races, the forum is our place for encouragement and help for weight control and other issues for the larger sized cyclist, like me (6'-1", 230lbs.) With your enthusiasm and new found cycling love you will do just fine, make sure the bike is properly fitted for you and ride safe, it will all come together for you. Best of Luck.
Bill
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Semper Fi, USMC, 1975-1977
I Can Do All Things Through Him, Who Gives Me Strength. Philippians 4:13