In reply to cameronwood:
Hey, I struggled with this for a while recently. It sounds like you're doing the right things, so I don't have much to add.
I think I decided it was a problem mid-August, went to see a physio, stopped climbing and running entirely. I was doing plenty of stretching and eccentric calf lowering (presumably this is what the physio has recommended to you?). It was pretty tedious, at least half an hour every morning and evening.
I started climbing again after three weeks because I had a trip to Lundy planned and booked. This probaby wasn't a great idea, as it was quite painful on some of the routes, and especially walking around with a 20kg pack on! However, it didn't seem any worse when I got back than when I left so I decided it was ok to start climbing normally. I noticed (prompted by advice from somebody else on this forum) that one of my pairs of climbing shoes was a lot more painful to wear than the others, so I stopped using them.
Now, three months later, it's not giving me any pain and I'm about to start running again, building up very gently. I went out on Sunday, 6km, easy pace. It was a bit sore in the evening, but fine again by the next morning. My inclination is that this pain was a positive sign of strengthening, rather than damage, but I'm going to go even more gently next time...
Not sure how much this will help, it's all very personal. To keep my sanity for those 3 weeks off climbing and running I hit the fingerboard pretty hard and started swimming again for cardio.