I am currently supplementing phytoestrogens (100% maca root) to try and increase my estrogen and progesterone levels. Is this something I should continue or put on hold until I finish the program?

For now continue with the maca (maca is something you should cycle (on 4-6 weeks, then off 3 weeks). Then as your GI tract and immune system improves, you should need less and less, because your body will be able to retain the hormonal balance the maca gives by supporting your pituitary gland. As your health improves, your need for things will decrease, but maca is a good, periodic go-to for energy, stamina, and thyroid health.