She ignores that and says if she is going to call somebody she's going to deduct it from the rent.

He probably will help out with the deductible or replace whatever was destroyed.

Our last years taxable income was a low of roughly $40,000 since we started a business.Based on my general calculation (not including deductions to make it easier for my understanding) we'll gain $112,500. 

We don't know your marginal tax rate or other sources of taxable income and deduction.

You want to ensure for the purchase price and have $2k deductible. 

April 30th we sent an email confirming that since they told us we would be reimbursed from April 5th until repairs are completed that we would be deducting April 5-April 30th pro rated rate amount from May rent which would equal to us paying $306 on May 1st and any deduction for May would be deducted on June rent.

Also, the interest paid on mortgages can be tax deductible, which makes the cost of borrowing much less.

It doesn't seem to have helped me much at all from a Tax standpoint; CPA noted that my income (from my day job) was too high to claim certain deductions.

If they move, then you clean up and deduct whatever you are entitled to from the security deposit. 

But essneitally she can make up to the standard deduction before a filing would be required- so you could potentially pay her up to $12k with no tax return.