If anything, it makes everything more complicated since you can't use conforming residential financing and have to run everyhting through the LLC. 

A conforming residential loan has to be held for 6 months for the lender to keep their profit. 

So work with a lender.Unless there is a specific issue (you mention “situation,” but not sure what that is) with your financials, any residential lender can originate the usual conforming loans

You can't use a conforming residential loan since its over 4 units so its not residential. 

I have a two flat in an area currently zoned R2 (two flats are prohibited in this area) however the code allows legal non-conforming uses to continue under certain situations. 2004 is the effective date of current zoning map but looks like my property was converted around to two flat around 2000 so I need to know if two flats were allowed at that time.

Honestly, not something I'd suggest unless you really *want* to do it ... but is less expensive and is how real estate investors make a living doing this.The first and most important thing to figure out is whether your current duplex conforms to current zoning. 

I own 10 Airbnb condos (legal, non-conforming) in a 40 unit complex.  

I own and live in a duplex (with a non-conforming third unit) in Seattle.

-Understand what a conforming vs non-conforming unit is.

However if a property sits vacant for a year or more, it loses it's grandfathered status and must conform to TNZD.