I personally use a CPA that I have been with for over a decade and she is phenomenal and always finds deductions that I would never find on my own (mind you, my taxes are also more complicated due to the nature of my work and the various investments I hold).

Double however, big companies have managers that need to think up complicated junk to validate their existence.

It's too complicated and confidential to mention it here. 

This can get expensive and complicated, as you had stated, which is where entities like the Series LLC can come in and simplify the process, allowing you to still operate assets within the same class in a single entity and housing them in separate child series for protection.In your situation I would have many clarifications I would want to make, but I will just spitball what it could look like.

Does it being a commercial property short sale make it any more complicated?

This complicates things now since it’s like me purchasing a SFR with a ADU and not as two separate houses since I’m sure the next buyers will want to have this resolved if selling each house fixed up to two separate owners.

Turns out its way more complicated to fill out then the current lease my PM is using. 

Complicated situation, here goes...My wife and I bought a duplex with my in-laws 21 years ago.

I think you are making this too complicated.

I had this issue with a Section 8 tenant (which is even more complicated) and heard all the nonsense month after month about her drama, sons drama, baby father drama etc etc.