Quote from @Carlos Lopes: Gross income doesn't matter.This is the number most people post, and it's 92.7% useless.What you need is NET income, meaning the money left over after all expenses, and that should include a dollar amount for your personal time spent operating the business. 

Besides your rent, your cleaning fee should be the largest expenses for your normal operation.

You should record the full rent of $2000 and show and expense/capitalize the $1000 payments on the roof. 

But you are also doubling the number of tenants, chance of expenses, etc.   

Expensive lesson learned but you will recover

I've included an example below to help illustrate this.So different lenders have different rates (which do vary even for DSCR loans) but these are factors they all consider.See example below:DSCR < 1Principal + Interest = $1,700Taxes = $350, Insurance = $100, Association Dues = $50Total PITIA = $2200Rent = $2000DSCR = Rent/PITIA = 2000/2200 = 0.91Since the DSCR is 0.91, we know the expenses are greater than the income of the property.DSCR >1Principal + Interest = $1,500Taxes = $250, Insurance = $100, Association Dues = $25Total PITIA = $1875 Rent = $2300DSCR = Rent/PITIA = 2300/1875 = 1.23If a purchase, you also generally need reserves / savings to show you have 3-6 month payments of PITIA (principal / interest (mortgage payment), property taxes and insurance and HOA (if applicable).

My worry is that while I am clear on the risks (extended timeline to get a tenant in, and expensive buildout) that I am not being nearly conservative enough - do I risk this thing sitting empty for a year, or years, and finally renting well below my implied rate? 

Then if at the end of whatever time you have agreed upon, if the tenant still has not left, you can get the Execution to move them out.There are programs out there that may assist the low income tenant with first last and security as well as some moving expenses at a new apartment.

That being said prepare for unexpected expenses. 

It’s on a 30-year mortgage with ~$130k remaining at a 5.25% interest rate. my monthly mortgage + expenses = 1,350/month and I bring in $2,800/month in rental income.