I'm sure your physio has covered this, but have you started walking lunges as well? I started doing lunges to generally strengthen my upper legs against recurring 'thigh splints' (adductor insertion avulsion syndrome) brought on high mileage on concrete with weak upper legs, and my adductors size and strength increased significantly. I alternated jogging, walking and lunging each time I did a session, keeping the number of lunges down initially to avoid aggravating the injury as it can place a strain on the adductors. Many other muscles in the upper legs will increase in size with these as well.
As maintenance, I still do 100+ lunges in sets of 20 after each run, and 50 or so in sets of 10 before each run, and haven't had the same problem recur.
Agree with lunges.....started doing these to help with generally strengthening/conditioning legs to help with recurring achilles problems....but I have noticed that since doing them, the old patella/infrapatella fat pad problem I used to have hasn't raised it's head since. I did some squats as well, but felt the most burn from doing the the lunges.I majored in walking lunges, while I was injured I just walked round the park doing 150 per session, 3 or 4 times a week, in sets of 10 to start, then 15, then 20. Just doing them with bodyweight was enough to make a great difference, now doing them with weights once a week to get stronger still. Don't overdo it at the start though, ramp up gradually over the first couple of weeks to make sure nothing else gets injured.
I agree, core work will help, plus what worked for me also were walking lunges and squats, loads of them. I've mainly had achilles problems rather than upper leg problems, but would occasionally have to take time off for thigh strains, including one where I seemed to be able to feel all the vibrations going up my femoral shaft while running.
With that last one, I rested for a month or so, then started adding in walking lunges while walking round my usual running route, and standing squats. Six months on, my upper legs now feel very steely and I am running three of four 10k distances every week, with no twinges whatsoever.
My legs weren't conditioned properly before - when I started doing the walking lunges I could feel a massive burn on the inside of the thighs after doing 10 or 20 lunges, and I was wobbling while doing them - now they're pretty easy. My adductor muscles in particular have got much bigger, which is bad news as my suit trousers will now go threadbare on the inside top of the leg where my legs rub against each other. Glutes have also got harder.
I feel more confident about avoiding groin/upper leg injures now - good luck.
If there's no swelling then it doesn't sound sound acute so ice probably won't help (but I'm not a physio).
Give it a few days rest, then before the next run try heating up the achilles/soleus with a gel pack before running - when I had a similar stiffness recently, usually my lower leg used to stiffen up at the start of a run and then stay stiff, but if it was warmed up beforehand it wouldn't ever develop to be too stiff over the course of a run. For me, over about ten or fifteen runs eventually the problem went away, as I guess the achilles wasn't placed under so much stress at the start of a run (cumulative benefit). I run about 30 miles per week.
Echoing the above, foam roller on the soleus (do all round it, back and both sides) and as Paul says, plant your foot on the floor and bend the knee - do this as many times a day as you can to keep things flexed up. And eccentric calf stretches, but go easy on them when you start - I did 3 sets of 15 with bent leg and 3 sets of 15 straight leg when doing my achilles rehab, and my soleus locked up in my right leg straight away, so start gradually.
Also, shoes may have something to do with it - I have some Asics GT-2170 shoes where my heel feels like it sits slightly below my midfoot, when I run in those (if I run without a heel insert) my soleus stiffens after about 3 or 4 runs (but the first couple of runs are very comfortable due to the overall good cushioning). When I run in my other Brooks shoes, my heel sits further up and there is less midfoot cushioning/thickness leading to a bigger 'heel to toe drop', and after a few runs in those my soleus stiffness goes away again. But all that maybe specific to me.