This projection will allow you to make your quarterly tax payments for the Federal and State on time. 

The safe harbor applies to amounts paid during the tax year to acquire or produce what the regs call a “unit of property” (UOP), you must meet these requirements: (1) at the beginning of the tax year, the taxpayer has written accounting procedures treating as an expense for non-tax purposes amounts paid for property costing less than a specified dollar amount (which will be 2500 for you), or with an economic useful life of 12 months or less;.(2) the taxpayer treats the amount paid for the property as an expense on its books and records in accordance with its accounting procedures. ( do this on your bookkeeping software or whatever you utilize)(3) the amount paid for the UOP doesn't exceed $2,500. as substantiated by invoice.Note: The cost for the Unit of Property includes additional costs (for example, delivery fees, installation services, or similar costs) if these additional costs are included on the same invoice with the tangible property.Eg:A purchases 100 printers at $500 each for a total cost of $500,000 as indicated by the invoice.

Additionally, you may want to see if you should be making additional estimated tax payments to avoid underpayment penalty.

That is why most sophisticated sellers want some down payment so they have money to make their tax payment. 

You may qualify for the small taxpayer safe harbor depending upon the property basis and your total repairs and improvements on the property.

The bill reads "if the average modified gross income of the taxpayer for the taxable year and the 2 preceding taxable years exceeds..."

Your questions are great, but not any that I can answer without specific knowledge of the taxpayer and the transaction. 

On a side note, if your uncle passed away after age 70 1/2, the IRA can generally be distributed over his life expectancy which will help your father in spreading out the tax payments.

To self-certify, a taxpayer merely completes a form (which will be released in the summer of 2018), and attaches that form to the taxpayer’s federal income tax return for the taxable year.

At that point however the LLC becomes the tax payer so it would need to do a future exchange and sell and buy the next property.