You have to weigh the cost payments of each and see, which is better or lower for you!

I could probably rent it for $750-$1000 per month over what the standard monthly costs are right now (not including vacancy, maintenance, management company, etc).

They may be easy and relatively inexpensive to add sub-meters for the secondary unit, or they may be significantly intertwined, making it much more costly to separate.

From my estimations considering vacancy rates, cost of maintenance etc - I would be at a cashflow negative of around 1300 - 1500 dollars per month.

It's harder to finance good properties right now for obvious reasons, and if you go NNN or DST then you need to be very clear about the costs (upfront and ongoing) that might eat at your returns. 

Used the 3% realtor commission as a credit towards my closing costs.

Asking $620k Debt service $4,352/m (10% Interest, 30-year amortization, 80% LTV) Taxes ($1033/m), insurance ($833/m), maintenance($1000/m), property management ($2400/m)Total - $9,613 (very rough estimate) Cashflow with 70% occupancy - $2,387/m (Cash flow pro-forma with adjustments $7,000/m+)What am I missing? 

A lot of CA investors go out of state to start because it's more cost effective and lower price points, look into markets like Detroit, Kansas City, St.

It's the cost of doing business.

Unit A is about 100 years old and Unit B is almost completely new.Pros:-The duplex is in a very desirable neighborhood with home value appreciation year over year at about 50+%-Rent is also in high demand within this area-Cash flows well even with high interest rates and increasing property taxes-Home is price below average cost per sq ft-The house has been renovated and some parts of it has been remodeledCons:-All issues are with Unit A, the 100 year old unit.