What does pain in ankle and bottom of feet come from having this for a while?

Many things: What type of pain do you have? Does it burn when you stand on the bottom of your feet? Do you have swelling in your foot and ankle? See a podiatrist for further evaluation. It could be tendonitis, nerve entrapment, possible stress fracture, foot and ankle strains. Meanwhile, try to ice and elevate as much as you can and get in and see a podiatrist or orthopod trained in foot and ankle.