This is about your risk tolerance, no one can tell you the "right" answer but yourself.Putting 20% down on a primary residence is a safe bet.

.- Depending on size of the property, scope of the work, and how much rehab you're willing to do, you can always consider individually submetering each unit.

Other things we would like to consider are pet type and size (we accept pets), references, income etc.. 

I am betting on income not appreciation in this market.

@Teho Kim, local/regional banks and credit unions are usually your best bet.

This strategy makes sense to me because of the value of my time as well as my ability to fund down payments on medium size properties (10-20 unit apartment buildings in C areas).

THIS IS MY QUESTION"    If you're contractually obligated to live in the duplex, you will have a hard time getting a mortgage for the second primary residence unless you have a change of circumstances like a job move or an increase in family size. 

correct - your fha loan will drop the MI soon  .....HELOC is your best bet ....most lenders want scores > 700 for  helocs ...make some inquiries  and make sure to mention  the mod and the solar panels  when  shopping for  helocs ....I would also  recommend  getting the  heloc in place for the highest amount you can  

LibertyShare or other Health sharing ministries are a good bet.

Basically, they don't want to take the risk that if things don't go as planned, having to chase you across the border.Smaller more local banks may be more flexible if you are buying 'small' properties but if you are looking for a mid-sized (250K - 2M) commercial loan - it can be extremely difficult.Good luck - Oren