I am experiencing a real pain in my outer foot about half way between the heel and toes. It started to hurt after climbing in a tree doing pruning. It has happened in the past when I have been scuba diving and also when I have been running in the sand barefoot. Seems very strange and it is extremely painful. I believe it has happened on both feet(thankfully not at the same time!) Any idea what this may be?

You could have a hairline crack in the bone, that heals and rebreaks. It might even be difficult to see on X-ray, but that's what I would have done.
Working in trees and on ladders means using your feet in unusual and stressful positions, so it might just be nerve irritation or a pinched nerve.