So, in essence, we treat the income & expenses as 3 separate units and we split the income & expenses 50/50 for the QJV and file the according Sch E's.

You need to operate the LLC as a separate entity, as that is what it is, with its own bank account and paying its own bills.   

Does purchasing a single family home that we would live in with a separate rental on the property count as house hacking for getting a low down payment and having the rental income pay at least some of our mortgage expense etc.?

Since it’s a 3unit and with full open basement with separate entrance bathroom and kitchen is there a way for me to occupy the basement and rent all 3unit.

If I'm understanding the exchange rules, we would need to purchase that lot separately for at least $523K to maximize the tax benefits and would we need to finance around $200K. 

A separate trust account is used to keep tenant security deposits in the clear.With regard to multiple property owners, your accounting software should be set up so that you identify each individual property, and, along with your chart of accounts for items such as property tax, management fee, insurance, plumbing repairs, rent, late fees, etc. etc. you make entries to the proper accounts.

They tore down the garage and built a separate 2 story building, at 800 sq ft (the max allowed for an ADU).

@Jennifer Maiolo I am going to run into this issue as well and researching options to meter separate circuits for energy use and either bill it back or contain a certain not to exceed amount in the lease.

So if you bought all quads... you could have 40 units with just 10 loans (80 if you are married and each person can qualify separately). 

Even better if they had separate entrances, parking and addresses.