If it was one mouse I might try the DIY approach. 

This gets complicated and is not a DIY project.And, depending on the specifics, various other limitations can come into play.

I choose the category (cleaning, repairs, utility bill, etc.), enter a description of the charge, list the amount, and add it to the ledger.

Any one have any experience in cleaning the soil or what it takes to clean it?

Ex: If a tenant calls up to complain that their drain is broken or running slow, or that a light fixture needs replacement, or to spray the Apt with insecticide, or to fix a broken door-lock or window frame, or anything of the like such as the fast repairing, touching up, painting & cleaning needed during a turnover between Tenancies...

Fully under AC, clean rooms for advanced manufacturing, excellent building in every sense of the word, from a tenant perspective. 

Since much of the house would be common areas, you might even consider hiring a cleaning service to go through periodically.

Over the last 15 years they have really cleaned it up.

We're interested in a place to live that breaks even with 3 units rented, has some value to add and is relatively clean in an area good for raising kids (no ghetto/near industrial, etc)  We have about 100k of skin.What are some areas worth focusing on?

@Ryan RuncheyAside from DIY approach and the outsourcing approach, there is a middle way, and it may be just be the golden path for many newer investors.There are companies that will set up your account, customize it according to your needs, train you on how to maintain your own books, and help with support or troubleshooting when problems arise.