The bathroom was pretty decent, so we were able to just get it professionally cleaned and the house was ready to rent.

There is one or more sections of possibly damaged/cracked drain line found under the home as viewed from the clean out at the front of the home.

Older buildings with older systems: plumbing, electric, HVAC, roof, tend to have more maintenance costs than newer properties.  

Agreed, last deal I had in Jersey city was lost due to really bad plumbing and electrical issues, on a older mixed use building. 

I found out they wanted to go to Atlanta to stay with family, I offered to pay for the flights in exchange for keys and within a week I got a squeaky clean house back.But, be careful: an offer of cash for keys can get your eviction case thrown out (in Wisconsin), so don't try both at the same time.

It could just be some roots in the sewer line that you can have cleaned out for $100-200. 

It has separately metered electric service. 

Units are metered separately for gas and electric.

My property manager then sent another technician who said the gutters need to be cleaned and recommended installing leaf guards around the entire duplex, along with larger downspouts and overflow guards, for a total of $3,013.

I did everything myself from cabinetry, drywall, flooring, windows, plumbing electrical, etc...