Additionally, flood insurance is commonly available and ensures that for an extra few hundred bucks a year, you're covered both for damage and loss of use (i.e. missed rents). 

Am I missing something major for this transaction?

I am a newbie in the whole repair estimation process so I am seeking opinions on what I am missing.

For me if it's anything more than cosmetic such as fixtures, paint, patching, or roof then I'm out.

What is this missing (if anything)?

My credit history is not great (missed couple of payments few years back) and I am having tough time securing a loan (borrowing close to million dollars).

Highly valuable to be sure, but also missing the most important parts...the connections to the rest of what you do. 

Maybe I am missing something.  

A few of my wife's pictures taken on 9/5 showed cracks on the cement floors (obvious that I know I didn't notice them when we first saw the house on 8/15), a ~8" chunk of cement missing from the 6" thick foundation pads on which the oil burning furnace sits, with the HVAC 8" inlet metal collar on it rusting already. 

However, it sounds like it's fully functional and just missing some modern safety features.