I would first want to know what your level of activity is. If you are engaging in a lot of high impact aerobic exercise, such as running, then it is likely that the intermittent pains you are experiencing could be related to this exercise. I do suggest seeing your primary care doctor
, so that you can have a complete exam of the affected body parts and figure out what is going on.
In the meantime, you may want to try resting from vigorous high impact sports and exercise. You can try icing the affected areas as well. Make sure you are wearing a supporting pair of athletic shoes, especially if you have any arch problems or trouble with over pronation. Taking anti inflammatory medications like ibuprofen or naprosyn is also ok.
Common causes of knee pain would include patello femoral pain syndrome (runner's knee) and iliotibial band syndrome. Common causes of pain in the middle of the foot would include plantar fasciitis. Your doctor will be able to help you figure out which, if any, of these conditions you may be dealing with and will also be able to help you decide whether any further type of treatment is needed.