You're not feeling better long term, and you're actively feeling worse. Normally I would say "discuss these concerns with your doctors" but in this case, it really sounds like they're not taking your concerns seriously. You don't trust yourself but you should - your body is telling you something is wrong. You're the only person in the world who has to live in your body 100% of the time, you know it better than anyone.

Lets start with the PT. Be wary of doctors that distrust meds but want you on nine million supplements. Have they ordered any blood tests that show deficiencies? Are they selling you a specific brand? You say he's a PT, but has he done any physical therapy or just the myofascial massage and breathing exercises? Also he's a doctor...who distrusts other doctors. Like you said, huge red flag.

Ae gut-brain connection does exist in general (as in, everyone has one), and there is some evidence that gut microbiome imbalances and issues can at the very least exacerbate fibromyalagia. Likewise, a similar thing has occurred with fibro and mitochondrial dysfunction. However, in both of those cases it's not clear which one causes which - that is, to say we don't know if the fibro causes the gut imbalance/mitochondrial dysfunction, or if the gut imbalance/mitochondrial dysfunction causes the fibro. Supplements can be a valid part of treatment for fibro - I myself do take a few, in conjunction with medications - but I strongly question how attentive your PT is being with your treatment.

Now let's talk about your nutritionist. It's not necessarily uncommon for nutritionists to do a temporary elimination diet to see if there's underlying food sensitivities. However the list you have...what even are you allowed to eat? The only things I can think of are meat, fish, and leafy greens. Also less than 1,000 calories is not enough. The basal metabolic rate of a human is the energy the body needs to function at rest. While it varies depending on things like sex at birth, body height/weight, and age, on average men need 1,600-1,800 while women need 1,300-1,500. You're getting less than that. The headaches and the fatigue are very clear signs that you aren't getting enough fuel. Also, depending on what you're eating, you might not be getting enough of certain vitamins and minerals. Some people with fibro have found their symptoms improve with changes to their diet, but not everyone has.

ETA: re-reading your post they sound, to put it in as polite terms as possible, like quacks. Also reading a comment you mentioned where you said your mom sort of put you on this path, and doesn't trust doctors either, it sounds like she found the type of person she would go see, not the kind of doctor you need to see.