Our estimate came in higher than we could justify for the property so we trimmed down the scope of work and are going to handle some of the lighter tasks ourselves.

Let's assume desirable neighborhood, close to public transportation, etc but no chance of ever qualifying for standard financing.  

How do I begin to estimate the cost to rebuild to determine if this is worth considering?

My problem with the 3rd (and easiest for the landlord) method is that could end up being quite a few people who don't have a chance of qualifying that end up paying a non-refundable background check etc fee. 

I did just find a company who does both and I think it's around 20% total, but I have not had a chance to speak with them to verify. 

I'm fine with with a super conservative estimate since something is obviously better than nothing, but don't even know where I should start?

I'm looking for a way to go through the DD and escrow period but have an out on the off chance that the financing falls through without losing my escrow funds.

Could it be estimated as original borrowed amount + interest that would have been amortized or is it likely to be some nightmare # like  principal + interest + penalties + interest on penalties?

You may get a chance to refi before the ten-year period. 

Zillow estimates the home value to be between $679,000 - $792,000, but I would be able to purchase it between $500,000 and $525,000.