Rehab achilles tendonitis - foot strengthening

I have had mild, but chronic achilles tendonitis (left leg) for a couple of years. I was told by a physiotherapist to use the exercises I had previously been given (to rehab a sprained ankle) to sort it out, but I didn't have much time for exercises, so I made do with a 10 minute session on the wobble board every 2-3 days. It was better than nothing, but not enough to cure the achilles.

This January it started to deteriorate to the point I was having to ice the tendon and wear compression bandages again, so I thought I really should put the time into the old rehab exercises. When I'd had the sprained ankle a few years ago, the most effective exercises I found were resistance exercises with a theraband. I have to wrap my foot in the band, which is tied to a table leg, then flex the foot against the furniture, doing x number of reps towards myself (central foot muscles), to the right (inside muscles) and to the left (outside muscles).

I started with 20 reps in each direction using a blue theraband, then worked up 1 extra rep a day to 50 reps. This was clearly helping the tendon - I do the knee-to-wall test to compare the flexibility of both ankles, and the difference went down from about 7cm to about 3cm.

However I then pulled a little muscle on the inside of the foot. I stopped the exercises for 3-4 days for it to heal, in which time, the tendon started getting puffy and stiff again. Re-started the exercises again (40 reps first day, then 45 next day, then 50, but I had to do them quite gently on the inside where I had pulled the muscle) and have just re-pulled the same muscle within 2 weeks. It is so frustrating, if I stop the strengthening exercises again, the tendon will just go rubbish again.

Please can someone advise
a) if I should stop for this stupid muscle to heal, I assume yes, but maybe it's not so important as I think?
b) if yes, how long I should stop for,
c) how many reps I should re-start with
d) are there any other exercises that won't bother the inside of my foot that would benefit the tendon?

Many thanks for any advice