I stumbled on a blog a couple years ago where someone said to read a book about zinc/copper ratios in your body. She said she healed hers after figuring out she was eating too much copper food. The book was called “Why am I always so tired?” by Ann Louise Gittelman, PhD.
She states in there that there are a lot of issues related to zinc deficiency, including Morton's Neuroma. Copper is very high in foods like grains, beans, nuts (including chocolate) and dried fruits. I was eating a lot of this food and also functioning more on a plant-based diet with occasional fish/eggs so it made sense to me that I was over eating copper foods. I was also hiking a lot and eating nuts and dried fruit for energy on the trails. She does indicate that even if you eat meat that you can still be zinc deficient if you're still over eating high copper foods. She also states in the book that you can take sulfur to help detox excess copper in the diet. MSM is a sulfur compound that may help with this condition.
After reading the book, I took zinc 50 mg twice a day and started eating more animal protein and cut back on the high copper foods and it went away within a day or two. That made me believe that this was the reason for my flare ups. Maybe this is not for everyone's condition of Morton's, but in case it helps anybody I thought I would let you know that it did work for me and it might be worth looking into.
The book has a lot more detail about it so it would be beneficial to read. It does not specifically talk about MSM just sulfur, but I recently read it again as I had another flareup and had forgotten what I had done before and saw the information on taking sulfur as well which I did not do the first time so I am trying out the MSM as well as zinc to see if this helps for long term results. Will update later on that one.