some people (like me) are born with excess fluid that covers the tendon sheath.

I found out about mine, when I had a hemangioma tumor removed from my left foot. It used to bleed, and was a mess...and was deep and it was painful to have done. (back in the old days before lasers).

Anyway this fluid shifts, moves, and can be irritated if you tie your shoes
too tightly. I have a very high instep which makes this worse.

The fact that your swellings change in size does not seem to me to be Charcot foot, which is more static, resulting from broken bones not felt.

As I have aged I have to be VERY careful of tie shoes, and slip ons cannot hit those tendons. If they get compressed or bumped they make my toes numb.
I cannot even get into most boots because my foot is so high. You also have to watch for broken sesamoids...which are in the ball of the foot. I have had two cortisone shots there over the years. When these bones shift slip around, you can get swelling and alot of pain.

It is really important to get a screening from a good podiatrist (some are not good).
Since your bone density is poor, I'd also get a blood test for Vit D. If you are low, calcium will not be absorbed well without D. Also low magnesium and low B12 negatively impact bone density. And new research also implicates low vitamin K for osteoporosis and poor protein. One problem with Fosamax and other bisphosphonates is
that it makes bones a bit denser but MORE BRITTLE and they don't heal well if they break. I think we will see less emphasis on Fosamax for this reason.

So there are many nutritional things you can do besides Fosamax.

One thing that really helps my feet when I have pain is Salonpas patches.
These are over the counter and good for inflammation pain (I also have arthritis).

Feet are very complex, and get alot of abuse and wear and tear. Many things can happen individually with them, and I think people should always consider multiple causes of foot pain. Just because you have some neuropathy does not mean you don't have other things happening too.