A long gap between BSc and MSc when applying for PhD
You do what you can with what you have. You have a record with some pluses and some minuses. That won't change. What you need is an explanation for why your record is what it is but that also suggests that you will be successful in future studies as the obstacles are behind you. 

In many universities there is an opportunity to personalize the application through interviews and other communication. Contact with a specific professor with whom you wish to work is often possible - and even preferred in some places. Having an idea about what it is that you want to study/research in a doctoral program is helpful. 

But in general, the time between degrees isn't a big problem. The low GPA in early studies isn't a huge problem if it is overbalanced by better performance in recent work. Having goals and good work habits is a definite plus. Knowing enough about a field to begin research relatively soon is very positive. Do what you can with what you have. Focus on the positives, not the negatives.