If we put money aside into a separate account for repairs/maintenance, potential vacancies, and capital expenditures, are these amounts tax deductible?

For expenses, I used the following percentages taxes 1%, insurance 1%, vacancy 7%, repairs 5%, capital expenditures 5%, property management 10%, mortgage depends on the value of the property ( I am planning to pay 20% downpayment).

It helps to have the extra capital for carrying costs, unexpected rehab expenditures and closing costs.

Many "operating expenses" taken by property owners are more accurately capital expenditures and should not affect your NOI for purposes of valuation.  

Just when you think you're cashflowing nicely, the HOA hits everyone with a special assesment for some underfunded captial expenditure.

In the PF he envisions expenditures to be ~$4.9M with a final profit of ~$3.4M.

This will help you identify areas where you could cut back expenditures and increase savings.2.  

I now oversee the renovations and capital expenditures of 124 communities in 4 cities throughout Texas of which there are residential, mixed use, commercial, and student housing properties.

Run the numbers on the BP rental calculator and make sure to input realistic numbers for maintenance costs, capital expenditures, taxes, property management, insurance, and finally the mortgage. 

If you you are factoring in expenses such as maintenance and capital expenditures, so your property is being kept up, you are doing your part to fend off depreciation.