I want to document my agent's and my own activities so I can claim the 20% Pass-Through Tax Deduction (aka Safe Harbor).

Property 1 - Sell the property (you could 1031 it to better performing properties, or DST, UPREIT, or pay the taxes, (maybe offset some taxes with charitable gifting, or other deductions depending on your tax situation)Property 2 - Cash-Out Refinance - Pull out as much as you can, do the repairs and increase rentsProperty 3 - Pay off the property with Refi money, do the repairs and increase the rents.You would keep the two better performing properties, improve cash flow and investment returns.If you want to keep property 1,  I would refinance it and pull out enough cash to pay off the other two properties and do the upgrades.

Instead of paying capitals gains tax you’ll get interest and depreciation deductions, as well as future appreciation.

Even if you don't get a refund from the amended years, if there is deferred loss you can deduct that from the profits of the sale (according to NOLO. 

At tax time, my tax person said that all my self-pay for contactor fee had to be categorized as a deduction on income taxes.

It looks like I’ll be in the $2,800 profit for July after deducting all expenses.

You'll see SchE has a bunch of categories for deductions... 

The problem with ACV is that, on a partial loss, the claim, under an ACV basis, has a deduction for depreciation.

I know the interest on the mtg for the homestead would be about 2% less and I'd only have one closing fee instead of 3, but am I missing out on any tax deductions for the income that these properties will produce by doing this?

@Shay Levy I recommend you check out this link it will help answer your question I think .