Those things just need to be reported to code compliance. 

The rental is the third least expensive in it’s zip code when I search on Zillow.

So, create status codes for both of these and a few in-between codes to help you work smarter, not harder.

This IRS code allows you to walk away with up to $250,000 in gain tax free ($500K if a married couple), and if that money can be invested for a better return(and ease of investment) elsewhere, it may be worth calculating.

And where your CPA may be worthwhile is reviewing your books at the end of the year when it comes time to file your taxes to make sure you're not breaking any laws, and that you are taking full advantage of tax breaks and existing code.

How do I check that the basement apartment meets the city’s building code standards?

In situations such as this, if it's a multi-family, an appraiser might use Gross Rent Multiplier and/or CAP rate and compare to other large multi-family properties in the town/city/area code. 

The first step we do is review the local municipal codes regarding a PUD (Planned Urban Development) or Re-zoning a property or Zoning a Sub-division, as well as the Comprehensive Plan. 

correct me if I am wrong but I believe if the sewer lateral is over a certain age that the city code is it must be replaced at sale .Ergo the mandatory aspect of it. 

We were told by the technician that it would have to be completely replaced and we would also have to have our chimney lined to bring it up to code.