Welcome to my world! I have sprained my right ankle 6 (!) times and now pretty much have chronic tendinitis. By staying patient and not pushing it the moment you think you are getting better (this is my problem and it will set you back several weeks of getting it under control), you can slowly etch away at the tendinitis. I have been to physical therapy for it a few times before and here is the program they have always put me on:
--warm up at medium intensity on a bike for 10 minutes
--stretch you calves and achilles (facing a wall, put the good ankle forward and step back with the injured side, lean forward until you feel a stretch--do this 30 seconds with your injured leg straight (then 30 with it bent)
--work on propioception exercises
a) balance on one leg on an inflated disc if you have one, or just use a few pillows on the ground, work up to doing 3-1 minute reps with your eyes closed).
b) do a wall squat, then raise one heel as high as possible while still keeping the ball of your foot on the floor, then alternate feet. This works the soleus muscle that is most commonly associated with achilles tendinitis. If this muscle is weak, the tendon is overworked.
c) place some pillows on the ground and work on stepping forward onto them in a lunge (forcing your ankle to stabilize itself). Basically, any exercise dealing with calf strength and ankle stability is going to help you out.
d) the best exercise of all is concentric calf raises: http://www.pponline.co.uk/encyc/0031.htm
--Ultrasound (if you have one?) or simply deep massage of the ankle
--15 minutes of icing
--at night, wear a night splint (I like the dorsal night splint--I also take it backpacking as it only weighs like 6 oz and it keeps me hiking).
I have mixed feeling about using a heel lift. It does have the advantage of relieving strain on the tendon, however it does this by further shortening the tendon which increases your recovery time overall. I've talked to physical therapists who love them or hate them, so it really is a personal preference.
They had me doing this every day. I can get it to the point where if I keep a moderate pace while hiking then I'm fine, but the moment I push it the tendinitis comes back. For the first week or two of thru-hiking this seems to work, after which the ankle is strong enough from hiking 10 hour days that I don't have to monitor my pace. I've hiked the Colorado Trail, the Camino de Santiago and the CDT using the above mentioned training/maintenance program. Now, the only time I get tendinitis is when I increase my mileage too quickly.
Unfortunately, I'm now a bit of an expert on this subject, so if you have any questions at all shoot away.