A couple of basic things to think about are running shoes and running form. I have not experienced what you have, but when I don't lace my shoes tightly enough, the bottom of my feet will start to burn from my shoes slipping around. I would make sure that you are not lacing them too tightly. Experiment to see if it changes. I also subscribe to the Chi Running style which has me landing on my midfoot when running so that there is less impact on my feet/legs/knees/hips. I also try to land with my foot right under my hip and not out in front. One thing I tried to simulate when I was learning this was to pretend I was running on ice. This is very much the form. But check it out and at least assess your form is and how it is impacting your body.

As I got introduced into running I would also mix up my runs where I was walking for lets say 1/2 mile and then would run the next 1/2 mile continuously building up my running base.

Good luck.

I have sprained my ankles and I have experienced edema from overuse and then not elevating my feet. I have done many things to heal and protect my ankles. Here are all the things I have done or am doing year after year.

1. Stretch, stretch, stretch and do yoga regularly
2. Proprioceptive exercises-one leg weight lifting (i.e. lunges, single leg Roman deadlift, single leg squat, pistol squat, single leg calf raises)
3. I wear zero drop running shoes and low/no heel shoes whenever possible.
4. Eliminate heel striking. Run with a light midfoot strike, always.
5. After a run or when travelling I wear compression socks. I will also make an effort to get my feet up. One way to do this is to sit on the floor with your feet up on the wall. This feels really good and your legs will feel better right away.
6. Ice, elevation, rest and even ibuprofen if the swelling is related to inflammation caused by an injury.
7. I am working on a vegan/vegetarian diet. I suspect this helps also.