You might also consider a private test to rule out celiac disease, given you have gut symptoms, if you haven't already ruled it out. (The GP might do it, but it sounds like s/he's not the helpful sort.) They are available as on line kits quite cheaply. Around one in 20 hypos are celiac, according to research, and obviously the risk must be higher with gut symptoms. I think it is worth excluding as a possibility.
If you are already totally gluten free it won't work of course, and gluten will not be playing in to your symptoms.
You could also ask for an h pylori test, if you haven't already had one, and s/he will probably agree to this if you say you have reflux and it is getting worse. Again, worth excluding the possibility that gastritis caused by h pylori is feeding in to your gut issues. It is a stool test at my GPs.
If you have been supplementing B12 and folate then that will skew your results. But if you have not, and your B12 test is low, you should ask for serum gastrin to be tested and also for anti parietal and anti intrinsic factor antibodies to be checked. This is to see if you have markers for autoimmune gastritis which coexists with hypo for around 35 per cent of patients, according to current research. My guess is the number might be higher, since it is very difficult to diagnose and the absence of markers doesn't necessarily mean the absence of the disease. But you have more than a one in three chance of having this and again, I would think that the probability is higher than that with gut symptoms.
Of course Flower is correct that your gut symptoms may just be down to the hypo. But you could go down this exclusion checklist if your gut issues do not improve.