I am so sorry that you are going through this.
I also have the MTHFR gene, and my Dr's attributed 3 m/c to this. Now with all of my pregnancies I take progesterone (another precaution having nothing to do with MTHFR) baby asprin and high doses of folic acid. I have not had problems since (knock on wood) with m/c anyway. I don't think I've heard of MTHFR causing any late term m/c... mine were all 1st trimester... but I imagine its possible. probably something that you would want to talk to your Dr about more. I was also told that the MTHFR can cause issues with clotting even when your not pregnant and it has been suggested that I stay on folic acid always.
Sorry that I couldn't offer any better answers. (((HUGS)))
OH wow all i can say is im so sorry !!! I personally think that the umbilical cord seems more of a reason for stillbirth, i do not think that a flu can effect an unborn child.