As far as the capital improvements, would I have to amend my 2017 return to fix this?

Will I have to file two amended tax returns?

Due to timelines and for simplicity sake we don't want to amend the purchase contract to be our natural selves, so what would be the most tax and legal advantageous way to do this triple transfer?

Make an Amendment, have your Agent send it over for signatures.

At a PSC meeting on February 12, staff will brief the commission on the Revised Proposed Draft, which incorporates their possible amendments.

Find someone who actually knows how to handle your situation correctly if you're just going to end up paying that old CPA, and than paying someone else to amend it. 

Do I make some sort of amendment to the existing lease or draft up a new lease with just him?

I paid the capital gains tax on my 2017 tax return, but now I'm wondering if I can file an amendment and recoup the amount paid, since it went into a QOZ. 

If the deduction is approved after your file your 2018 return, you can file an amendment to claim the deduction.

I stupidly did not have a must close by date on my contract, they have offered to give  me more escrow to extend the closing, and I have this opportunity to have the contract amended I believe, and add it must close by _____, and demand more escrow, to protect myself.