Hi there Susannah, from someone who has suffered from a long term back problem I have found that in order to minimise the affects of running on my back I have to take a few precautions.
Stetch properly, thats all your legs muscles and your back muscles.
Only run on roads in races and never more than once a week.
Build up mileage very slowly, follow a hard week with an easy week, a hard day with an easy day.
Make sure you have the correct type of shoes for your running style.
Also the pain in your knee may be caused by the tightnening of your muscles down the side of the leg (ITBS)
Hope this helps, if it gets worst a visit to an oestopath or similar therapist may benefit you.
Jane.