Your hormones will eventually balance out. Keep in mind that you have been overloading your system with progesterone for a long time. All of a sudden you are dropping that excessive load of progesterone. So your body is going to go a little crazy with this sudden drastic change in your hormones.
You may want to look at this, which could explain some of what you have been experienecing:
Focusing on your adrenals right now would be a good idea to help you deal with the stress you are going to deal with as your body readjusts itself. The adrenals will also help with balancing out your hormones. I would add some licorice root to your regime for a hormonal adaptogen.