I too suffered with achilles tendonitis for a couple of years. I did PT for 3 months, which helped a lot. In addition to the exercises, My PT, also a cyclist, also had me do:

1. Use Heel cushions in my everyday shoes. I used these (still do):
http://www.drscholls.com/drscholls/p...p&searchArg=48

2. Lower bike seat, and slide it back on the rails accordingly.

3. Moved cleats on my bike shoes back a little bit.

I got quite a bit of improvement in the first few months, but it did take over a year to be back at 100%. Probably would have helped to continue the exercises longer, but, well,......

Good luck.