Check for any building permits done.

In fact, there were two code violations that I was made aware of at the closing (so money was held in escrow for the repairs) but there were several more I was not aware of until I went to get permits for the two that I did know about.

You can also check to see whether the property has any existing code violations, what permits were pulled, even whether the 2-family is a permitted use (don't assume that it is).

The 'hold my hands' ones are typically more expensive with versions of design, fixture choices, designs for permit submissions, etc.    

I went to the city to see what permits I need to build a build and hook up the water to the meter.

We always permit them. 

The unpermitted work was the concrete deck the last owner illegally put in, and the city's code calls for 40% landscaped areas in residential lots and he was at around 75%.The other houses that did it did without permits. 

The idea is that people building new cabins in the area need to secure small chunks of water rights in order to be get a permit for a well which they need before they can get a building permit.

He built a whole second floor, it was not permitted.

I would not suggest building a spec home, as prices of permits, labor, and materials are such that you can hardly build a new house for much  less than you can just buy one for....