The ultimate intention is to make it inhabitable. 

If the units are inhabitable now, rent them out and focus on cutting costs.

making your unit only inhabitable by the owner. 

This program is a non agency, 20% downpayment and min loan amount $50,000 (hopefully a banker will take that small loan) and properties have to be inhabitable, no distressed properties.

Are the properties you are looking at inhabitable (even if they are not somewhere you personally would inhabit, would they qualify for a conventional loan?)

Basically any duplex that is inhabitable has been getting snatched off the MLS for a premium. 

Both have their pros/cons.The journal Square area is good and you can get into NYC in under 25 minutes.I think the area has already experienced significant price increases over the past couple of years.Live-in-flip is good cause you are looking at a property that needs to be fixed up which can translate to a cheaper cost compared to a house in excellent shape.You are also eligible to exclude a portion of all of the capital gain if you live in it for 2 years and then sell.You would need to keep track of all the repairs/improvements you make to the house.A con would be is that the house has to be in habitable condition prior to purchase otherwise a bank won't loan on it.

@Leonard Burks you can do the 203k easily with 3.5% down; roll all closing costs as seller concession, yiu can refi or sell after the reno to get rid of the mortgage ins, also you don’t need to make mortgage payments during the reno of the property is inhabitable.

Assuming the house is inhabitable, you can get conventional, FHA, take out a HELOC and use it to buy the house, whatever. 

I am also looking at properties that are are close if not fully inhabited at the time of purchase so there is (hopefully) immediate cash flow.