Neurological/immune/digestive issues - would appreciate some guidance

Age - 28
Gender - Female
Height - 160cm
Weight - 45kg
Ethnicity - Caucasian
Duration of complaint - several years
Location - Eastern Europe (childhood), Britain (last 5 years)

Hi, I'm writing this query on behalf of my girlfriend who has been suffering from a range of problems for a while now and has tried to get herself healthy without any concrete sign of improvement. On some days, I feel that she is getting better (though it's difficult to measure, and the more deeply-rooted issues appear to still be), on others I'm concerned that her state may be affecting her endocrine system and could affect her neurological health and thus body's ability to self-heal and her mental health and hence her willingness to self-heal.

She has had a number of problems with recurrent infections (throat, constant phlegm etc.) throughout her life as well as sensitivities to a variety of foods as well as environmental factors - can't drink cold liquids, seems to have a strong response to sunshine (nb oddly this is not just light, she is fine indoors and with artifical lighting, it only seems to be a problem outdoors and is a more recent development, last year or so).

She is unable to work and increasingly rarely goes outside, but I'm fairly certain that due to the presence of infected phlegm and certain other concrete symptoms (a feeling of heaviness 'like stones' on her chest and occasionally on her sinuses) that the problem is not neurological in origin, although some symptoms may be the result of consequent neurological issues. She has numbness down side of her body sometimes, and a lot of trouble sleeping (she wakes up frequently at night to pee, each time she passes a lot of urine so it doesn't seem to be anxiety-related).

The problem is that she is now very reluctant to travel to the doctors' because a) she finds it very tiring b) she believes their actions/misdiagnoses in the past have made her situation worse c) she thinks they are only treating the superfices and not the root cause, and I think she has a strong case for this.
When she suffered from acne some time ago (about 5 years), she was on a course of antibiotics that made her temporarily feel better (and helped clear the acne up), but then got much worse soon after. I imagine this could be something to do with not being advised to take the right probiotics, or a badly managed regime generally (I don't know the details).

Her fairly reasonable interpretation is that she essentially nuked (or imbalanced) her gut fauna leading to a whole host of other problems including infections and subsequent anxiety. Trips to the doctor resulted in her being put on antidepressants (sertraline, can't remember the initial dosage but I believe it was less than 100mg), which helped her enough to just about be able to work (which seems to be the main aim of antidepressants) but led to her feeling like she was in a kind of artificial bubble. The positive feelings did not feel real, and meanwhile the other problems suggestive of infection worsened. Doctors, apparently, could never find signs of infection though.

She weaned herself off antidepressants over a course of about 6 months, slightly reducing the dose at regular intervals until she hit 0 around 18 months ago. About 6 months prior (around the same time she tried cutting down) she had begun a Candida diet too, as a number of tests had suggested she had overgrowth. I was skeptical of a lot of these tests (as I still am to a lesser degree) but thought it was worth trying with a pinch of salt as I'd also become rather skeptical of and disillusioned with mainstream medicine, or at least that I had experienced (in addition to the above, I had been prescribed treatments for migraines and anxiety which turned out to be manageable purely by introducing a more restricted diet).

A few months later (approximately a year to the day) her period stopped, which may have been because her weight was quite low, or could have been because of stress. A lot of the controversial buzz theories - adrenal fatigue etc. - came into diagnosis, and why not? We had yet to find a convincing theory elsewhere, even if this one was ambiguous - at least the treatment seemed to be largely dietary.

Regarding the periods, she was referred to a gynaecologist who organised a few tests and bone scans. The latter found that her bone density was slightly low, the former found that she had low estrogen and so was prescribed Femoston Conti. She has not taken these for two reasons a) she does not feel her system is strong enough (and hence is afraid of a negative reaction, which is perfectly understandable given her hypersensitivity, even if it might not be the right decision objectively) b) she believes that the treatment isn't missing the root of the issue. We have another gynaecologist appointment in January where we'll be able to discuss this in greater depth (the one in May seemed to serve the dual purpose of being instruction to two trainee doctors, thus we didn't really feel able to make our points and enter into discussion as we'd have liked to).

The last six months or so have been relatively quiet and it's difficult to tell whether she's making any improvement based on her diet regime (pretty much a paleo/FODMAPs with certain irritants excluding), at least no new symptoms have emerged.

To summarise the main current symptoms (in approximate order of severity as I see it):

* Insomnia - or, rather, broken sleep due to the need to urinate large amounts relatively frequently resulting in around 4 or 5 hours actual sleep in 8 or 9 hours bedtime.
* Weight loss - She had dropped from around 52kg to around 45kg over the past 15 months or so (the degree drop in itself isn't worrying, but her present BMI is - late teens).
* Constipation - she eats quite a healthy amount (no sugars though) as she doesn't want to lose any more weight. This, it seems to me coupled with the general sluggishness and malabsorption of her system, might lead to her being 'backed up', and she often eats despite having no appetite. She reports that she feels irritable/depressed often, and feels much better when she managed to offload cargo, leading her to feel that toxins are causing her to feel in such a way, though this may be rather naive/simplistic (though my skeptical position works both ways).
* Sensitivity to smells - notably cleaning products and foods with antibacterial properties (onion, garlic, spices etc.) - certain foods, and sunshine.
* Difficulty breathing - at times she struggles to get full breaths in, especially when/after eating.
* Mood problems - she often feels very down and can become anxious (though not acutely), or argumentative (more acutely) as a consequence of the above symptoms. This is compounded by a sense of hopelessness that she might ever recover.
* General aches and pains - particularly in her back.
* Excessive mucous creation - especially in the morning, she often has to hack up phlegm.

It is interesting to note that her acne has almost completely cleared up since she started her diet, and other issues which were more severe in the past seem less so now, though it's important to recognise that she's also cut out a number of the known irritants.

I'll finish by adding that she has done a number of tests through a range of providers from those supposedly less reputable (Cambridge Nutrition) to those who are slightly more reputable (Cyrex, Genova, Acumen), at least among those who give credence to any of such services.

The tests which she has taken include:

* Cyrex Array 12 - pathogen associated immunity screening, which suggests that she has excessive (though not necessarily to the point of acute infection) numbers of acinobacter, strepococcus mutans, citrullinated EBV, klebsiella, and babesia + ehrlichia + bartonella (or presumably just one of these?). We only got the results of this test last week, so we're still processing what exactly it means.

* DNA adducts - notably some type of benzyl/benzoate and parabens, which might explain the sensitivity to chemicals (and subsequent moodiness)?

* IgG tests - I realise the validity of these is still under question, but she has nonetheless taken them and they do generally match with her personal feeling of what she has problems with (with a couple of oddities), and also seem to have slightly improved in the 2017 result compared to the 2016 one.

Particularly re the pathogen test, it might be of use to know that she grew up on a farm (relevant assuming obviously that our hypothesis about the infections largely stemming from the antibiotic treatment is incorrect) and did not always receive cutting edge medical treatment for e.g. being bitten by a stray cat when she was young, and also lived in a house which had damp problems with people who had/have their own health problems (some of her father's are very similar, in fact).

There are more tests (and we're planning to take Cyrex's Array 5 - autoimmune issues), but I realise I'm writing a plea for help, not a book, so I'll stop there. Obviously my concern is that I want to help her get better, and thus am seeking open-minded advice of a 'holistic' nature, at the risk of coming across a bit 'alternative' (my point is that consideration of the whole situation is important, rather than narrowing in lazily on certain details, as we've felt people have in the past).

Any advice on a direction to take, preferably accompanied by a convincing-yet-sympathetic argument (a difficult ask, admittedly), would be much appreciated. I realise that some of the narrative we have constructed may be contradictory (i.e. potential origins suggested at different times), but I'm just trying to be as objective and open-minded as possible.