How to avoid personal issues interfering with my Ph.D. studies? Background

My life had (and still has) difficult problems (chronic disease and its consequences: social isolation, anxiety, having to take extra measures to take care of my health...). As a disclaimer, I am in psychological therapy right now. 

That being said, I managed to finish my bachelor’s degree (mathematics, with a very uneven transcript with both very high and very low grades) and after that I did my master's degree, this time with very high grades. I did my master's thesis and then I was offered Ph.D. admission by the same research group in which I did the master's thesis.

To the point

Now, the problem is that I am constantly reevaluating if I should do my Ph.D or 1) either find another program or 2) move outside the academia, and I am unable to make this decision due to the fact that I think personal issues are interfering. I identify several more or less objective problems:


The Ph.D is in an applied department (biology), which is formed by specialists in the area, I have been told the research group is good in its area by a professor from another department (from the same university) which I trust, but since I am a newbie and have little knowledge about the area, I cannot test it myself. I have been here for 6 months.
I did not choose this Ph.D. They chose me. I think ph.D students are actually scarce where I live, and that is a reason why they hired me. I feel I could be in a more satisfying Ph.D program or area.
It is likely difficult for me to get funding in other Ph.D programs due to the problem stated above. This Ph.D is the comfort zone, I have funding (this is Spain, where even in private companies salaries, for graduate students with no experience, are not that high).
I feel like academia is a good fit because it allows me to work without a fixed schedule and in a non stressing environment. Note that I have not really worked outside academia.
My Ph.D supervisor is great, I like her as a person. But although she is a mathematician, I sometimes feel like she left mathematics and now she is a biologist more than a mathematician. This is leading me to think she not the right person to supervise a mathematician, past Ph.D students are happy with her, but most of them have biology related studies. Also, 
She chose a Ph.D subject which is now in stagnation. I warned my Ph.D supervisor about this likely outcome several months ago and she told me to trust her, up to a point where we showed we could no longer apply the technique (a particular machine learning technique) we were trying to apply to the topic, leading to now being trying to publish a result so that the time employed is not lost. I now feel as if we were trying to desperately find something to publish from a technique that has proven not to be effective. Not to mention that reading through papers in biology is difficult, as I find myself not understanding lots of things. 
I have enjoyed research, but not most of the time, I fear this has to do with personal problems not letting me concentrate, when I should be reading papers, I end up procrastinating with the phone or forums. I can concentrate when I like what I am doing, but not right now. I also do not feel like I have a strong passion for researching in a particular topic.
I am also concerned about overspecializing in a particular topic that leads me to not being hired afterwards.


So the question is, How can I make sure I want to pursue a ph.D?,  i. e.  pretty much what title says, I want to avoid personal issues interfering with the decision.
The problem is easier than it seems. Your first responsibility is to yourself. What you most need to do is find a way to build a life for yourself that you will enjoy over the long term. This could involve a PhD or not, however, you seem to really be attracted to Academia where a doctorate is required. Earning the degree might actually be the sacrifice you make to achieve your goal. But keep the "good life" rather than the PhD foremost as your goal. 

A number of things in what you say indicate that you might profitably look at a different subfield than mathematical biology. You can use your current position, as well as your past education, as a base from which to conduct your search, speaking with other potential supervisors and even institutions. Don't underestimate the value of a good supervisor, of course, and she may be able to help you if you approach her in the right way. 

Having been chosen, rather than choosing is possibly a big part of your problem. You "went along" at a point at which it might have been better to "take charge". This led to a number of your other dissatisfactions, I think. But you can take charge without making a clean break at this point until you see something that you really want to do. 

Also, since you were chosen you should have confidence that your skills are not in doubt.