I honestly don't understand why you even consider to leave.
Most of what you say is relatively normal. For example, It is rather uncommon that supervisors beyond the post doc level have the time to show you techniques in the lab. Most of them probably haven't been working in the lab for quite some time and are therefore anyway a bad choice to learn new techniques. Most of my PhD colleagues have a meeting with their boss every 4-6 weeks where results and future experiments are discussed but besides that, they are on their own. You can always ask colleagues for advice but to some extent you just have to acquire the knowledge yourself and try it.

Your PhD is going so incredibly well that you could write up and finish in 1.5 years. This is exceptional, whether or not you knew the techniques before. If you are really annoyed by the environment and your supervisor, then my suggestion would be to write up and search for a follow up position that provides you with more training opportunities. With a PhD in 1.5 years (many struggle to finish in 4) you should have no troubles to find something new

First of all, I think it is already impressive that you made it this far despite these massive set backs in the project and the difficult personal circumstances. You can take pride in that. Many people would have quit by now.

Now that you are already over the 3 year mark (I just assume 4 years funding), why not at least try to write up and attempt to finish? In my opinion, there is not much to lose now. Have an honest discussion with your supervisor, where you also mention the difficult private circumstances and maybe there is a way to make it a thesis, even though the project was supposed to go further. Most theses have chapters where everyone involved knows that this manuscript is never going to get published. Chapters with negative results are quite common and as long as there is something (you mentioned one published paper) that worked, it can still pass. I would at least discuss it with my supervisor. Maybe he or she has an idea how to make it work.
I think it will bother you eventually if you quit so close to the end without exhausting all options.

Sometimes you also have to accept that certain things are just not for you. Some people need structure in their daily life and do great things when they have it. Others do exceptionally well if they have a lot of freedom and can organize their time themselves. Friend of mine studied a humanities subject that required very little university attendance. Most of the time you are supposed to do research for your assignments, which he always did last minute with the result of mediocre grades. He just couldn't motivate himself to start earlier at home. He often started few days before the deadline to work on an assignment they had 3 months for. Another friend of mine absolutely thrived during a similar degree and probably did much more than the degree required him to do. They are both intelligent. To some degree it is just personality.
You seem to have analyzed the issue quite well and know what the problem is, yet you didn't manage to change that behavior in 27 years. Unlikely that there is some magical technique out there. You just have to pull through and do it, but you already know that ;)

Do you really need that PhD to achieve your career goals? If not, maybe starting your own business or working as a consultant would be the better choice.

It's hard to say something without more details regarding location or field of study but in Germany for instance, it is normal to get a 50% (around 1200€) to 65% (around 1500€) positions in the life sciences. I never heard of any scholarship that provides you with more. You are of course expected to work 100%. Only fields where it is really hard to recruit PhD students such as computer sciences will offer higher salaries.
It's of course disappointing if you expected a higher salary but in most of central Europe you should be able to live comfortably with 1500€. I know many PhD students that are located in Zurich and can promise you that even in Zurich, you'll get by with 1500€. I know several PhD students from South America and Asia personally, who came with their own scholarship that is in this range and they spent 4 years in Zurich. And no, there are no rich parents in the background that could afford to sponsor their child ;) You will live like an undergrad without any luxury but you can certainly manage to get by. I am however relatively sure that they will adjust the amount of money to the Swiss living costs. At least it was like that for a friend of mine with a French scholarship.

Personally, I would suck it up. If you have enough to make a living (and 1500 is enough) then it is all about the institution, your bosses, your project and the colleagues. That's what is impacting your mental health in the end. More money is always nice, but I guess you didn't get into a PhD program to earn a good salary ;)

It is a bit hard to give advice without knowing anything about the kind of financial issue you are in. I respect that you don't want to talk about it but the responses might be more useful with a bit more information.

How much money would you need compared to the 18-20k and what are the chances to land a fulltime job after quitting your PhD that pays you the amount you need? You mentioned that it would be hard to find a proper job with your background.

If there is absolutely no way to reduce your expenses or increase your income then finding a better paid job and quit the PhD seems to be the only option. In that case I wouldn't worry too much about the company or your supervisor. PhD students quit all the time and supervisors are prepared for this possibility.

I think it's quite evident that this is all not like you expected it to be and doesn't make you too happy. Being just 5 months in, quitting isn't so dramatic. If you quit after 5 months you can just say you realized the topic is not for you bla bla bla. In most cases this is not seen as a failed attempt and won't hurt your career. You wanted to change something, took initiative, it wasn't for you, so you are changing again. Perfectly fine. This gets of course more difficult the longer you are pursuing the PhD. I am now 1.5 years into my PhD and have to say that if it is not overall a positive experience, it is not worth it. Too often you read about the PhD journey of people and it reads like a period of suffering and anxiety that you somehow survive and that's the value you can draw from it. If there would be great job opportunities afterwards, I would accept that as some sort of necessary evil, but there aren't. It is highly competitive and most people don't end up in research careers but in jobs you don't need a PhD for (and even having a harder time to get those jobs compared to non-PhDs). I am not saying that a PhD is always fun, but if you don't like to go to work and feel anxious during long periods then there is something wrong, even though many people seem to think that this is normal and kind of like you have to feel during a PhD.

Do some thinking if this is really what you want. Doing it just to avoid that "fail-stamp" is not a good reason to continue ;) Good luck!

You are probably not the first guys to look at a disease using a sequencing approach. If you are absolutely sure that it does not matter, then maybe you can find some papers to support your point. It always helps me when my supervisors propose something that I don't agree with ;)