Currently the house is full of personal items from someone who recently passed away. 

There was a BP podcast where one technique was for the investor to get bids before purchase and then add those as line items to the HUD and get checks to the contractor issued at settlement (with the investor holding them until project starts or designated draw schedule).

You would need to have some sort of paperwork stating that the items on the property were in good working condition when they moved in and they acknowledge it.

Send a copy of your receipt for the repair items into the water company with a note describing the leak.

So, for example a bathroom remodel quote might include everything except the fixtures and flooring materials because you need to choose those and the price of those items could vary a lot based on the choice.So, I would clearly define the scope of work you expect from the contractor and look carefully at what is or isn't included in the quote.

I dealt with this on one of my projects, where the contractor gave me an incredibly low $/SF like that, but left out a ton of line items and wasn't able to stick to budgeted numbers on several of the ones he did include.

Certainly not something that I would run scared from, in fact, you should be able to use the engineer's report and suggestions to renegotiate a credit or price reduction for these hidden items.

You will need an overall design for each room and a punch list of items (that can be substituted for other items as the decorator finds certain things that work well and other things are not available in your budget).Expect your decorator to have to do a lot of Shopping and looking and meeting with you to come up with the right stuff for the look you want.

My flip has a very similar issue to item 1 (caused by bad plumbing in this case) and the repair was quoted at half your price and included replacing a foundational beam as well.

However it takes a ton of effort to get these properties up and running-  we just finished the desert and it was a 6 month reno, and we are still waiting on items like a garage door.