When a cost segregation study is also considered on the newly acquired property, additional analysis is recommended before finalizing the Sec. 1031 tax basis calculations.

Upfront expenses and monthly payments must be considered when calculating the return on your investment.EXAMPLEYou cash out $100,000 of your equity and use this as a down payment on a $400,000 investment property.

for our smallest property he did some quick calculations and came up with approx. $150k hit on a $550k sale price. 

It does not apply to 1- or 2-unit properties.Income Calculation: To conduct the test, FHA requires that the estimated rental income from all units, including the one in which the borrower will reside (if the borrower is not occupying the unit as their primary residence), be calculated.

I calculated rent estimates using both BP rental tool and Rentometer.com so the larger side will rent for average $550/month per room. 

BiggerPockets also has a calculator to analyze deals, and I highly recommend you start this as soon as possible, even if you are not ready to buy.

Cash flow and taxable income are separate calculations.

Unless they allow future rental income to count towards the DTI calculation.

Did you calculate the value of the time you spent on this?

At closing the taxes will be calculated per day and then divided by days remaining in the year at closing.