J.B.
Yes, first get your knees checked! You'll know what you can do safely after that. I have a left knee that gives me a lot of trouble -or it used to. At some point there is probably a knee replacement in my future. However, learning proper running technique REALLY has saved both that knee and my right heel. I always ran heel to toe, and you should really land/strike on the pad closer to the front of your foot, roll to the toes and propel yourself that way. I can't tell you how much that added to my runs! I just did my first half on Sunday.
Another thing I've done over the past year that has been instrumental in no more knee pain or injury has been intense weight training. I use kettle bells and go to a certified kettle bell gym. You can do a variety of different types of weight training, but building the muscles in your core and legs will really help you. Building the muscle strength around the knee and in your legs really helps end shin splints, knee pain and ankle problems.
Good luck!