You honestly sound like an ideal candidate for a PhD program, at least in terms of your mindset. Your career goal is essentially research and/or a research-flavored position (whether that is fundamental or applied research is largely irrelevant), and you have come to that conclusion based on your experiences. This seems about as cut and dry as these sort of cases come.
The issue of going back to living on the stipend is real, and is why people rarely go back for a PhD. However, at the very least, there are a lot more fellowships out there available for PhD students than there are for MS students, and your experiences and background in the field likely means you could write a compelling application. That could ease the pain a little bit. It still will be a pretty jarring change, though.
I can definitely say I knew several PhD students while I was in graduate school who did have kids and start a family while still in the program. It isn’t easy (and now that I have a kid of my own, I have no idea how they found the time), but doable if it is important enough to you.
Best of luck.