If your shins and knees just started to act up the cause could be a couple of things. When was the last time you replaced your shoes? They should be replaced every 4-6 months depending on weight and distance/week. Also visit your local running store and get fitted for a shoe. They can prescribe a shoe for you wether you supinate or overpronate while running. I know this sounds stupid, but I used to get shin splints and ITB irritation almost to the point where I couldn't walk. A few days after getting fitted for shoes everything went away except for a dull pain in my left shin. If you just increased your distance and speed you might experience a little pain for a while until your body adapts. Lastly make sure you are stretching well. The problems you have are usually brought on by poor choice of running shoes, tight calves, tight ITB, and running hills or increase in intensity.
Keep in mind I'm no doctor, however for the prevention of an injury that would take a few weeks to fully heal I would take a break from running for a few days and do a little bit of cross training. When your shins and knees feel better try running till you feel pain, stretch, repeat. Also do a search on ITB syndrome, shin splints, and chondromalcia to see if these apply. Also check out the book "Complete Book of Running" and its associated web site http://www.runnersworld.com for additional info.