Hi,
I had a similar problem. I had been running for a long time but only two three times a week and never longer than 10k. After I started running more and more often, I started experiencing all kinds of problems in my feet and ankles. I ended up going to a podiatrist and got insoles made. After that, most of my problems just disapeared and the ones left I can cope with.
I think I was pretty lucky as my podiatrist is also a serious runner and really knows how to manage "feet problems" for runners. The insoles (which were not cheap) had an inmediate and visible effect, but having a chat with her about running shoes also went a long way to improve my confort when running.