How often does he have low-grade fever? does he still have it?
I assume the stool test is for the H Pilori, a bacteria. I am surprised they didn't mention this https://my.clevelandclinic.org/health/diseases/21463-h-pylori-infection But I don't see fever as a symptom. https://www.mayoclinic.org/diseases-conditions/h-pylori/symptoms-causes/syc-20356171 No fever mentioned.
It might not be too late for an antibody test if they agree to do it. But a GP here on Mumsnet said clearly that they don't test for viruses. You can try to ask and see what they say.
I found this, about an MRI to investigate abdominal pain https://www.radiology.ca/article/why-would-i-need-abdominal-mri/#:~:text=Abdominal%20MRI%20provides%20detailed%20pictures,of%20abdominal%20pain%20or%20swelling.
A few pieces of information about what can cause stomach pain, besides covid https://ada.com/covid/covid-19-symptom-stomach-ache/
''Because mild stomach issues are not as common as some of the other hallmark symptoms of the disease, such as a COVID-19 cough or fever, it’s easy to dismiss stomach pain as something other than COVID-19. Alternatively, severe COVID-related stomach pain may be initially identified as a more serious condition, such as appendicitis, pancreatitis, or gallbladder disease. Because of this, if you are experiencing stomach issues and suspect you may have contracted COVID-19, it’s essential to take a COVID-19 test.'' - NHS never asked children to test for covid, so I don't see how they would suddenly take it into account later if they can't even see how essential the initial test is. But this website also mentions other conditions that can cause stomach pain.
If serious conditions are ruled out, they need to test for inflammation. If inflammation is to blame, medicine to reduce inflammation should help. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9600357/
If the gout microbiome is affected (even if it is, it shouldn't cause sudden episodes of strong pain), good gut bacteria can be found in fermented foods.
This is information in BMJ - any UK doctor has free access to this information:
https://www.bmj.com/content/385/bmj.q842#:~:text=6%20In%20severe%20cases%20this,the%20bowel%2C%E2%80%9D%20says%20Griffin. Griffin is a British virologist , can be found on Twitter
Many ideas and lots of information: I assume if they already found/suspect a cause or sent you for some investigations, you might not need them. Good luck!