This is not an "arms length transaction". 

Both sell and buy side will be $1 million+ each transactions. 

Why not go to your title company and ask them to scrape a list of all cash sale transactions over the last year where the purchaser was an entity and where that entity bought multiple in one year.

Find out how he or she wants to book these types of transactions and then stay consistent with that method.

Is there a way to structure this transaction to not invalidate the exchange?

Talk to your town first to see if you can legally convert to a duplex, zoning department.   

Rely on your coach/trainer or broker for your first transactions.

Work with a lender to figure out how much you can afford, what the best loan product will be for you, and what the cost-side of the transaction will look like.

Check with County or City building department on what can be built.3. 

I believe this company I'm speaking with right now said that they give free Re-fi after this transaction.