Start out with less mileage and build your way up slowly. It takes your ligaments/tendons/muscles time to build strength. This is particularly critical if you have a few extra pounds. That can really put the stress on your joints.
Also, don't jog more than 3 times a week in the beginning. Walking should be fine. Try to cross train (bike, swim, lift weights).
Keep taking Aleve or ibuprofen for the anti-inflammatory elements. I would not characterize this as too much medicine if you are a regular runner. Just make sure to not take huge doses and drink lots of water with it.
Ice your knees after a run.
Research/buy better shoes. Find a place that specializes in running shoes. We have a couple here in Seattle. You might be able to find one in Boise.
If possible, find a running trail that is not on pavement. Run in the grass or dirt, when possible.
Good luck and great job!