For example newer steel roof, plumbing, water-heaters, three baths updated,appliances, flooring, some electrical updates ect..

Usually the electrical and plumbing is a cost problemOn the surface $90,000 for the property and $1,500 rent is very good.  

It doesn't need any work to be habitable however I plan on spending about $5000 to update the electric, paint, floors, kitchen and appliances.  

You need to find out how each unit is addressed by the tax assessor's office, post office, electric, water, cable, phone etc...For example I have one property where the mail goes to 201, 203, but the water and sewer bill goes to 201 #A and 201 #B, yet the power company has two meters where one meter is attached to "201-203 North" and "201-203 South". 

How much is their deposit and how much are your charges for painting and redoing some of the electrical problemsHow much of the deposit are you refunding them? 

My brother and I sub'd the roof, stucco, concrete, flooring, electrical and plumbing.

Roof, HVAC, plumbing, electrical, or just age of the homes in general.  

The original PM (now fired) didn't take a security deposit from them and with all expenses, water and electrical bills etc. they have left me with an outstanding debt of around 2200$.

It's worth getting into a relationship with a contractor who is willing to come along and do some detailed work about kitchen bathroom, plumbing electrical, foundation, roof, etc, and a number to go along with each in exchange for hopefully getting the job or if not, a fee for the work done from you.   

That 1, 2, 3 combo fixes 90% of little, nuance troubles and the home warranty covers appliances, hvac, electrical, plumbing, etc calls with only $75 out of pockets per event.