What cities/areas should I be focused on?

@Trevor Carli have you tried reaching out to anyone involved in the Brew City meet up?

There are metro taxes if you are in Louisville of about $400 annually (not sure about other cities). 

If you perform the repair personally, you have to be reasonable in charging fair market rate. eg. if it takes 1 hr of your labor for some handyman's work, $20-30/hr is reasonable, even you're probably paid much more in your own line of work.My suggestion is to first fire the PM who obviously wanted to skim some profit by inflating the repair cost while exposing you to lawsuits (remember you're in CA - a blue state and San Jose - a city with rent control).

For our family that is our biggest expense each month.

Looking for grade A neighborhoods in cities across US.  

I think you should be able to check with the city to verify that the 3rd unit is legal or not before buying the property.

Other markets I like are Dallas, San Antonio, Jacksonville, Savannah, Columbia, SC, Indianapolis, Louisville, Cincinnati, Columbus, Oklahoma City, Tulsa. 

@Kong Chen Oklahoma City might be a good fit for you!

Sometimes I struggle with southern NH and if you can expect any rental growth above inflation - I understand it's proximity to Boston (but you're looking at least 1+ hour commute) and that prices in Boston and surrounding areas are continuing to drive people further from the city.