Stretching will cause injuries if you do not warm up properly and is of marginal benefit.
I have some suggestions for you:
1) Get a stack of Glucosamine/Condriton/MSM. The one I suggest is "Move Free" as it has the largest dosage of MSM. You can find it at CVS or whatever drug store.
2) Go to a professional running store that does gait analysis and have them look at the way you run and fit you with the best shoes for you. You wouldn't just buy any tires for your car, right? They would have to be the right size/type. Do the same for your feet.
3) If you are restricted to home and need something to mix up the running with, there is a very inexpensive piece of cardio equipment known as a "Gazelle." It has no impact involved. Here is a link to one for under $100 to get you started in your search:
http://www.walmart.com/catalog/prod...125&product_id=1597237&path=0:4125:4134:56687
I've used one of these and they are pretty stable and kind of fun.
4) Join a gym and take advantage of their expensive eliptical machines or spinning classes. Maybe try to find a pool. I don't know why you are restricted to your house but if you can scrape together the dimes for a gym membership, I'd suggest it.