They are occupied with paying tenants and I've owned them for almost 3 years.  

Input what fair market rent is for the one you will occupy, that way you compare properties the same. 

No matter where you focus, you'll have company.I buy single family homes in one target zip code, drilling down into a select few neighborhoods by a development I believe is going to create extreme appreciation and elevate the type of tenant looking to occupy the walkable dwellings.

I would be inclined to say that this very well taken care of/newer, 100% occupied complex, that is located off of a highway in a town of about 100 people would fall in the 7-8 range for Cap. 

If the vacant unit is too small to occupy (eg I have 2 kids; I need to occupy the 3b unit instead of the vacant studio) you have a case. 

I guess my question is, has anyone had any success lately using their VA Home Loan to acquire their owner occupied multi-fam?   

All the other houses on the street are owner occupied and they all take great care of their houses and yards.

Anyone know the implications of trying to convert a FHA/conventional owner-occupied mortgage to an investment property in the case that my partner and I would want to move somewhere else but retain the property?

I have really liked this strategy, as owner occupied loans get the best terms and can get a nicer portfolio with less cash down and lower interest rates.

Let that be your first endeavor- let it occupy the desire you have to invest, for the near future.