If you do stretch it's best to do so after the muscles have warmed up. Stretching cold can actually have the opposite effect that you want, and can increase risk of injury.

If you have pronated feet that have been supported by orthotics, barefoot running may worsen any issues you have, as you are in a state of imbalance, with those muscles that support the arch either not doing their job, too weak to do their job, or too tight and knotted to do their job. If you start barefoot running, the issues going on with these muscles may worsen. Of course there is the "other hand," where people think this will kick start your feet to a more balanced state. Only time and research will be able to sort out barefoot running risks and benefits.

If you don't have a bump on the tendon and it's about the same size as your other tendon and not painful, you've likely already had a reduction in your inflammation.

A great way to loosen your calves without aggravating the tendon is to foam roll. Also great to do when warmed up as it seems easier, less painful, and more effective. Here are some resources:

Fitter First’s Foam Roller Exercise Handout at http://www.fitter1.com/Assets/pdf/Fo..._Exercises.pdf
National Throw Coach’s Association Foam Roller Handout at http://www.nationalthrowscoachesasso...FoamRoller.pdf
Sport Medicine Institute’s A Guide to the Foam Roller at http://www.smiweb.org/roller.pdf
Foam Roller Exercise Video at Foam Roller Exercise Video - YouTube
How to Build a Foam Roller at How to build your own foam roller
Video on How to Build a Foam Roller at Make Your Own EXTREME Foam Roller - YouTube