Warming up prior to stretching, yes. You need to have warm muscles prior to your pulling on them. I usually go for a 5 minute jog around the neighborhood or lightly skip rope. It doesn't have to be hard core, just something to warm the muscles.
Try to avoid running on hard surfaces. Always take asphalt over concrete because it is slightly better. Run on the sand, track, trails, beach, etc. if you have the chance. That is a big relief on your knees. Good quality inserts are a plus. Most people just use the shit inserts that come with the shoe. Toss those fuckers. Most physical therapists will tell you the same thing. Try a pair of Sorbathane or SuperFeet, found in running stores.
And finally, look into joining a local track club. Mine is only $30/year and offers world class training several times a week. Plus they hold events and fun runs. The coaches tailor workouts to your goals and needs.