It was built in the 50's and the owner pays water, gas, electric for the property.

Does anyone here have experience investing in or putting together oil and natural gas exploration investments? 

Paint - $1kPlumber - (reseal bath tubs and sinks, check for leaks)Appliances - $2k

Now it is leaking around the skylights.

Maybe its time to schedule the HVAC filter change..... or say you found an issue with X (leaking window, crack in tub, peeling paint, bad flooring....whatever....) in the unit your are fixing and want to check if that's an issue is going on in the other unit too...lots of easy ways to have a look inside.....which you should be doing anyway on a regular basis unless you like suprises

The flower bed had weeping holes for excess watering; the water would drain out and leak into the drainage system in the middle of the garden. 

Plus a lot of other expenses are missing: I don't see water, electric, gas, lawn, etc...

Tenants pay for water, gas and electricity2.

The current unit is 21 years old and leaking freon.

The only reference I have is for my duplex and triplex properties in CO; sewage, water, garbage and share common area fees paid by me; tenant pays gas and electric.