Mold, mildew and rot

We bought our home in October of 2014. Before purchase there was an inspection done and airborne mold test. The air test passed and the inspector assured us the problems we pointed out with the floor were minor imperfections and of no concern. Then he mentioned we were always welcome to hire a structural engineer to do their own inspection if we chose. Problem number 1. We should have. Because last week after strong storms, a tree fell on the house. During the repair process we have discovered our sliding door was installed improperly (long before our purchase of the home). Due to the improper installation and incorrect pitch, water run off has been going directly into the wall and the floor and foundation. Now the floor is rotting through and soft enough that our contractor said he could jump and end up in the basement. Problem number 2, my dog pulled down a piece of (vinyl maybe) panelling in the mudroom to expose the drywall underneath shows definite water damage and something growing on it, mildew or mold I don’t know how to tell. This room is on the exact opposite side of the house on the bottom floor. Our basement often feels damp and smells musty so we have a dehumidifier running nonstop. The mudroom I mentioned is below my four year olds bedroom so I am concerned for her health, as well as my infant. My home owners insurance says none of these things are covered and we are a one income family. I don’t even know where to start with trying to remedy all of this and get rid of this problem. Money is a major issue but the health of my family and our home is priority one.
What do I do? Where do I start? I’m so overwhelmed please help!