I've searched quite a bit on the internet as well as seeing a PT about the issue. This is the best article I've read on the subject: http://www.runningwritings.com/2013/11/achilles-tendonitis-in-runners.html

In regards to stretches and exercises, you need to strengthen your ankle and calf as much as possible as well as increase flexibility.

Here's a good vid for stretches:


Watch this video on YouTube