I came up with $50, by subtracting the prorated rent from Nov. 1 to Nov. 18 and late fee from Nov. 4 to Nov. 11.How much (if any) of the security deposit would you give back?

Take the amount they are charging you, and subtract that from the amount your report shows, and what is left is the interest they are trying to add on top.

So take the price you want to pay and subtract all that out (Agent, repairs) and throw him the offer.

Since Listing agents almost never give sq/ft for apartments buildings what I've been doing to get a rough idea of apartment size is to access the local assessors site and get the building size, I then subtract 10% for common areas and then divide the remainder by the number of units.

Subtract the lost rents and costs to get the property performing and include a risk factor. 

Subtract 30% and I am still well above the 1% rule.  2 of the units were actually redone before I bought it, and the other 2 just need carpet and paint. 

I sold a rental house in 2015 for a 55K gain (after subtracting costs of sale, upgrades, etc).

Then no deductions are added back or usedYou have a rental history on your taxes, then your deductions are added back to counter the expenses.Here the calculation your should be getting using your schedule EGross Rents; minusTotal Expenses;plusInsurance; plusMortgage Interest; plusTaxes; plusHOA; plusDepreciate;Equals your subtotal (X) of eligible incomeDivide X/12 (months)=Y (monthly eligible income)Subtract your current PITIA from Y= Z - Your total income available to offset your increase your DTI.Do this on all your property and you'll know your total net income available to add to your application.So yes, once you do this calculation, we wouldn't add additional expenses to your DTI.

How do you add that option to a purchase contract and what is better a land contract/ installment contract where a dollar for dollar is subtracted from principal or a standard mortgage agreement PITI? 

Subtract your expenses (Taxes and Insurance, property management and some small reserve for maintenance) from your projected gross rents and subtract your mortgage payments over the year and get your net cash flow.