Get a second master to have better references?
I wouldn't if I were you. Of course grades and reference letters matter but to spend another year or two putting yourself in debt just for reference letters seems like a lot. You will also be two years older, and with no guarantee to get the position you want. I would try to apply for PhD's anyways, or if needed, try to find a project for a few months in the group/area you are interested for the PhD. In Europe there is funding for exchange students/projects. I spent a year in Sweden after finishing my MSc. back in the Netherlands. This was paid for by a stipend from my supervisor in Sweden.

Doing a project will allow you to see if this is the topic you want to do a PhD in, and also if this is the right group. If you do a good job and the supervisor has money for a PhD student, you can apply. If not, you can apply elsewhere using this supervisor as a reference.

Good luck.