(Had we rebuilt the original windows we would have been fine and wouldn't have had to bring them to current code.)

Depending on the lender (bank or alt. lender) you have to look at origination fees....points, doc prep, interest rate, frequency draws are allowed/min. draw amount allowed per request, interest payments vs. interest reserve & whether interest reserve is capitalized to fully understand the true cash requirements.

I would first separate out the original purchase price between building and land.

He ended up having to sell the home instead of renting it out, which wasn’t part of his original plan.

If I add up all the lender fees and my holding costs—like points, origination fees, and interest —I can figure out how much profit I’ll make and what my maximum offer should be.

So you might as well be a head of the game do the cash out refinance buy the next 1-2 properties and simply refinance the original mortgage as a "rate and term" which carries a lower rate.

they make money servicing not originating new loans. 

According to @Andy Sabisch's original post, I think he is asking for advice on how to confirm the veracity of the neighboring tenant's claim.  

Understand Replacement cost versus original building costs. 

Of course unless your buying defaulted notes at the get go then again as Chris mentioned this type of fee should be handled up front.. and if it new origination your making and then they go bad.. in your foreclosures you can charge the borrower these fee's when they cure or add it to you opening bid and when someone buys it at the court house you get repaid..