On the other hand, I don't want to saddle an otherwise good tenant with unnecessary eviction-filing costs when they are only a few days late with the rent.There is not RIGHT or WRONG solution for slow payers. 

You're in a 'problem' market but found a fantastic solution; out of state properties! 

My guess is she will find something wrong with your unit, and it sounds like her solution will be to not pay you rent.

I looked at perhaps buying a larger house and subdividing it up but anything I look at is just not feasible.My solution to this would be to obtain an FHA 203k construction loan and just build what I want, when I want it without waiting month after month hoping that something comes up. 

Depending on the scale at which you plan to implement the software, I do recommend for large 3rd party solutions, supplementing some of the current software short-comings such as inspections, and maintenance asset tracking.

This is probably your best solution.

The solution works well - a testament being that it is used by several turnkey sub-metering service providers.  

I can tell you how I account for these things but I am sure that my method is just one of several solutions that may fit your circumstances.First, repairs fix things that are broken.  

If you only have 1 property to keep track of every month, I think a simpler solution is warranted (I don't have any rentals so feel free to correct me).  

This way your no longer a part of the problems, deterioration, and suicide of your societies and you become a part of the solutions.