The total square footage for the house is 3857 sq/ft.  

Estimating the renovation is the hardest part in my opinion, there are calculators and prices per square foot for each different job, but I have found the actual costs to vary significantly.

A few nuances here related to the numbers:List Price: $449kFirst Offer Received Buyer X: $465k w/ $95k down (with appraisal continency) Final Accepted Offer from Buyer X: $480k w/ $48k down (appraisal contingency removed)Bad Appraisal: $440k (should have been appealed with ROV due to errors but buyer declined; average age of comps was 11.5 months and no inflation was added to adjust values, also appraiser used incorrectly small square footage)Buyer's Original 90LTV Loan: $432k ($480k w/ $48k down)Buyer's "Final" Loan Application: ????

We can find a stable 5 cap in Rittenhouse Square or drive a mere 2 miles into North Philly - for example - and easily get 15 caps, albeit much riskier.

When finding comps make sure that your comps are within a few blocks (Philly is very block by block specific), within 20% of your finished square footage, similar bed/bath count, and also a rehabbed property.

How could some possibly build a full unit, I am assuming is around 800 sq foot for free? 

If they are under 7 foot tall...

And the funny thing is, both appraisers might conclude the exact same opinion of value for the property.Price per square foot is not a useful way to valuate real estate, so you can't make the argument that you overpaid.

I watched Brandon's youtube video using the 4 square method and my CoC Return was 40.4% vs using the excel spreadsheet punching in the same numbers but coming back 10% lower.

Are you working with a TK company or you have someone acting as your foot on the ground?