Wow, that is a lengthy post
. When I hear an issue like yours, I always want to get back to basics. While the pain is in your foot, the problems are likely in your core. I see this quite a bit because as patients, it is natural to look at where you hurt but unfortunately, as doctors, we are also guilty of looking at where you hurt rather than why. We need to ask ourselves why are the calves tight, arches weak, etc and why did if feel better barefoot while you developed some other issues.
Usually, a torqued core will create this. A week ago, I visited a local running store that I refer back and forth with and he was having problems. He is a pretty strong willed gentleman so I am often surprised when he listens to my suggestions ( he makes like he wont but he surprises me). The other day, he said his back and hips were all messed up and he is a shod runner. A while back he complained of achillies tendon issues and a podiatrist gave him custom orthotics.
Upon evaluation, his core was torqued ( which will cause many of the problems you described in your feet), he had tight it bands, quads, hip flexors and gluts. I did some work on him as a favor on one of the benches in the store and set him up with an off the shelf insert (the custom one's were done poorly and were not helping him, even though he was compliant (sound familiar.) ). I have no idea if he had a mortons toe however I can make some assumptions based on your experiences.
1. You are built asymmetrically.
2. You have tight gluts, your core is distorted (look in the mirror, is one much higher than the other?)
3. Your upper body is tight and you hunch your shoulders when you run.
To understand the reasons behind this, you may wish to read my book Cheating Mother Nature, what you need to know to beat chronic pain which is available through Amazon.com
Things you can do to relieve this.
1. Find a good sports chiropractor (they do not have to necessarily be barefoot friendly, they just need to understand body mechanics)
2. Use a foam roller, check out our video on how to use this for runners here (
http://www.youtube.com/user/ChiropracticNJ). Also check out our video on joint capsule stretches, since your's are likely very tight.
3. If the hips and legs do not feel right, consider other aerobic activities that day since running poorly will likely make you feel worse.
You may also want to see my recent post on this here
http://www.backfixer1.com/blog/are-weak-hips-and-lower-leg-injuries-related-dr-c-weighs-in-on-a-runners-world-article/
I hope that helps. Since a Mortons Toe is developmental, it is likely not something that created the problem but you can have it helped with an orthotic that has a mortons toe extension built into it (just a thought)