> The pain has been in her arm for many years and, in my opinion, represents neuropathy.
It's not wrong to put commas where shown, but it also works without them. I cannot think of a case for just one comma.
> The pain has been in her arm for many years, and in my opinion represents neuropathy.
I don't like the version above. That's called an Oxford comma. In my opinion, there is no need for it, but the jury is out still on the Oxford comma. So, as you can see, there is a lot of leniency on this subject with your specific example.