I'm in a similar position--I'm 58, 32 years poz, although I did take early HIV drugs such as Zerit and a few others. I also had a near-death experience with Nevirapine, which caused anaphylaxis. I started getting neuropathy around 15 years ago, but it's advanced to polyneuropathy, including losing mobility in my feet and ankles. I also had a spinal cord stimulator implanted to help with the persistent pain.

I found it helpful to remember that HIV drugs, as far as we know, cannot pass the blood brain barrier, but HIV does, and may also form deposits in certain areas, just as lymph nodes. Blood tests are just that--limited to blood. They may show viral levels as undetectable, but we can't really assume that means HIV is inactive, or not still grinding away elsewhere. Why your stomach? I'm not exactly sure, but there is a close connection between your nervous system and your gut, according to recent reports about depression. The muscle pain you're feeling could be how you're perceiving neuropathy--not everyone has 'numbness and tingling'. Similarly, your headaches could reflect either HIV activity in your central and peripheral nervous system, stress, or a number of other things. I don't think there's any way to pull the threads apart, to determine what causes exactly which symptoms.

I'd keep talking to your neurologists, keep looking for new research, and try to keep up any exercise and a healthy diet. I've heard people find some relief by avoiding alcohol, and others sugar. You might also try mindfulness training or meditation, as a way to deal with pain, and not let it govern the rest of your life.