I then settled on making an offer on two different condos in a different city.

If more than one person will occupy the room, you want 50 sq.ft. per person (two people = 100 sq.ft.).You should contact your fire marshall or City Zoning and see if they have occupancy standards established.

My name is Sean Dawson, I am a biggerpockets member and have been analyzing multifamily deals in the outer areas of the Twin Cities using the biggerpockets calculators and ran across a triplex that looked promising.  

I've been to phoenix plenty of times and its a nice city, haha I spent more time thinking about moving there and leaving the people's republic of california than thinking about investment property.

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).

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.