Here are some really good stretches for your chilles and calf muscles to help with the transition from traditional running shoes to either barefoot running, or more minimalist type running shoes that encourage more of a forefoot or mid-foot strike which will be better for your knees.
These stretches have cured my runner's knee and allowed me to resume running. I hope they help you as well. I am not a physical therapist or a physician and any knee problem should be diagnosed properly by a physician. These helped me greatly.