Flipping a cat infested home

[Felicia Angelia]

It's an early 80s home and a major mess. 

There's old cat feces everywhere, noticeable urine stains, scratched up walls, black mold on the walls, rotten window sills, doors made out of wood and chicken wire that apparently were built to block off hallways, a tree partially through the roof in the living room, holes in the walls in some places, refrigerators that are beyond disgusting and vanities that are barely standing among other issues.

The place has a lot of potential I think once it's cleaned up but I've never tackled this kind of situation before. The floors are just the subfloor and will definitely require a good scraping to get all the nastiness up but I think they can be salvaged for the most part if I clean them up real well and use Kilz Maybe? Same for the walls?

What's the easiest and least expensive way to repair where the tree hit the roof? I don't think the structure is damaged or weakened (no leaning that I can see) but just holes where branches came through and plastic lining dangling some.

For the black mold, will using bleach water to clean it all up suffice?

Will opening up all doors and windows allow it to air out enough and then will using Kilz and paint (floor - only Kilz, walls, ceiling) help eliminate the smell?

I think the rest might just be deep deep cleaning. Any advice is greatly appreciated!