For example, construction grade carpet throughout the house besides in the kitchen and entryway which are engineered hardwood ( that has seen its days).

And send him some pics of clawed up doors and pet stained hardwood floors. 

When we ripped up the carpet we found original hardwood floor in most of the house.

I tend to prefer the beat up houses at a steep discount because I can know for sure that the hardwood, hvac etc I put into the house is going to last a long time.

Ramjack told me the best way to fix the issue would be to take up all the floors and rebuild the floor joists to get the floor level, but I didn't want to rip up all the hardwood floors.

Is there he water damage from extinguishing the fire (there are original hardwood floors)Could someone please provide insight or guide me in the direction of someone who could check this out?

Depending on the market your flip is in, you may want to go with a high-end finish like solid hardwood or tile, which require specialty tools and tend to be more difficult.

I also paid for the hardwood floors to be refinished and the exterior aluminum siding to be painted and repaired.

Hardwood floors throughout main living area.

Assuming a complete subfloor replacement and hardwood or vinyl plank I estimated 10-15K which might be over the top but flooring isn't cheap.