Submitting comps or upgrades that were missed with written explanations of why they should be considered, or evidence of errors.Person to speak with would be with the lender involved.The square footage thing will need to be resolved.

The cash flow on the property is good, but having a major upgrade like that would be tough. 

We don't rent to new section 8 typically because units need to be upgraded with minor fixes and tenants don't meet our renter requirements with credit and so forth usually.

My guess is depending on the electrical AMPs of service you have you may need to upgrade the electric panel to install electric heat. 

Maintenance was deferred, and a storm + a broken boiler drove out all the residents.

I specifically state in my lease in bold that "if the lease is broken for any reason (this includes leaving early) then the security deposit will not be returned."  

Why waste money upgrading when there's no benefit to you?

Last year, it grossed $50.6K, despite one unit being rehabbed for 4 months due to a broken water heater.

Someone had broken in through the back slider door and stole anything and everything of value, in which there was apparently a lot of gold and rare coins, crystals, and cash.

(And you don't need to go further to explain that the principal is broken down to the % gain, that gets into telling them how to arrive at thier tax liability and is beyond the scope of a Realtor or buyer making an offer) :)