I intend on purchasing the Flipster software, that way I can figure our the exact numbers.

Processing refinance loan applications has hit capacity.

If the inspection makes you want out of the deal, just let your lender know you won't be completing the application, and then let the seller know you will be unable to meet the financing requirements, so that they can move on quickly. 

Remember to screen your applicants well, an ounce of prevention is worth a pound of cure. 

we also saw an increase in vacancies and a significant drop in the quality of applicants on those same units during that time. 

To follow up on what @Guifre Mora said, here are the main things I would look at since it is a 3 unit and a quick breakdown for analyzing it.IncomeRental income  -Vacancy/Loss to lease (depends on area but 10% of income would be a good general figured to go with)Other income (if applicable, might have coin washers/dryers since it is near a college)Total IncomeExpensesProperty Management Fees (10% of income)Repairs and Maintenance (10-15% of income)Real Estate Taxes (can find on county's tax assessor's website)CapEX/Reserves (Can vary greatly based on condition of the property, roofs, HVAC, etc. 

Hopefully I'll see applications in a reasonable fashion. 

As the loan application queue lightens  up we will likely see a the bond and mortgage markets realign.

As you said property management rental analysis might be boosted and there is a chance that the two companies uses the same software for analysis in the background which explains why they came up with the same figure.

Once the bookkeeper helped setup my accounting software, (we use quick books), I took over the bookkeeping responsibilities.