I would double-check cleat location and seat height. Also find a knowledgeable physical therapist. Achilles can go south and take for freaking ever to heal. Really, like months and months. And I stress the 'find a knowledgeable p/t' part. (or chiro or whatever). All the achilles stretches in the world it turns out were the wrong thing for my instance, they would have just kept making it worse. p/t gave me different exercises farther removed from the source that kept me biking throughout and solved the problem.