I think a few of us commented on your pointed toes. If you walk around on your toes in the house it won't take long to feel it in your calfs. I think you may have identified the problem, which is pedalling style. You may have to concentrate to change it and I wonder if going clipless will help you keep your foot flatter. it may now be worth going back to your bike fitter to ask if he can solve this problem. I think clipless or putting your seat quite obviously too low, or both, concentrating on keeping your feet flat until you adapt and then slowly raising the saddle back could work as a plan. Keep your rides short while you do.
So it was! Hah. So much for my reading skills. I still think that could be the answer though. Simply adjusting your toes may just have taken the strain from one area briefly. Which shows the affect of such a change. I think experimenting with this and doing some stretching and massaging of your calfs might well be the answer. I think you've more or less proven that bike setup is having a minimal effect, so the answer has to lie elsewhere.
I think it's one of those things that you may need to try several things before you get to the bottom of. As an example, I started back this April from Patella Tendonitis. I just started on the turbo and after 2 sessions I had some pain in my right leg above my ankle which was completely random. The next time I got on the turbo I paid some attention to what I was doing and I realized I'd been pedalling unevenly, slightly toe down and when I did I could feel it. As soon as I flattened my foot, the pain went. Not completely. Several weeks later and that area is still slightly tender, just from two 20 minute sessions.
If you do want to get sorted, get a bike assessment from a physio. Who can check you over and assess your position on the bike, not an Evans salesman. Usually costs around a ton
