Stretching not only increases flexibility but can also be a vital way to avoid injury. I always start my post run recovery with some static stretching for about 15 minutes. I stretch my major muscles groups. I focus on my quadriceps, hamstrings, IT band, upper and lower back, groin, and hip flexors. I slowly ease my way into each stretch and hold it for 45 seconds. I then take a 30-45 second break and then do the same stretch again before moving on to a different stretch and muscle group. There are a lot of stretching information online but Runners World has a great list here, Flexibility Training. Here is a good site with step by step instructions on static stretching.
Another self massage tool I like to use is The Stick. The stick increases flexibility, accelerates recovery, reduces muscle soreness, stiffness, and pain. Similar to a foam roller but easier to do and you can control the pressure better using your arms and hands instead of body weight. The correct stick for an individual can be determined by a combination of that person's size, muscle density, pressure preferences and how the stick will be used. So, to help you choose the right Stick for you, they have created the Stick Selector. I use the sprinter stick because it is less flexible than the others and I feel it gets deeper into my muscle. The travel stick and marathon stick are favorites of several of my running friends. I think it works better when you can relax and let someone else massage you with the stick.
One final tip, do not pop ibuprofen and painkillers post run or pre-run so you won't be hurting during your run. "There's nothing inherently wrong with inflammation," says Tom Etges, a family physician and acupuncturist based in Eugene, Ore. Yes, you read that right, ibuprofen junkies. "The body is a lot smarter and more elegant than we give it credit for, and up to a point it will repair the damage if you let it," Etges explains. The medical community warns overuse of an anti-inflammatory medication can interrupt the normal healing process and cause liver damage. It can also cause a false sense of relief, so you're more likely to challenge yourself before you're recovered and ready. If you're in enough pain that you feel pain killers are your only option than perhaps you need a break from running or at the least a cut back in intensity and mileage. I would also recommend seeing your Doctor and a physical therapist.
Instead of forcing out potentially helpful inflammation, aid your body in flushing out superfluous inflammation. Drink plenty of water, elevate your legs above your heart for a few minutes whenever you get a chance, foam roll, increase your protein intake, and consume more anti-inflammatory foods. Whole grains, healthy fats from avocados and nuts, beans, leafy greens, and wild-caught fish promote an anti-inflammatory response in the body without the potentially long term damage of pain killers.