A toilet can be $ 100 and a handyman shouldn't charge more than $ 100 for install.

Consider how many people you are willing to have before charging for extra people.

When prices are so low you need to be super diligent upfront as an unexpected capital expense can tank all your profits. 

So if you lived there for 3 years, they shouldn’t charge you.

You definitely don't want a situation where someone gets hurt by traps or poison that you place.If it is more related to the tenants being pigs than a hole on the outside then it may require some education on how to keep things clean and charging them for pest control if local law allows it etc.

So my question is how can I protect myself if I do take charge of the apartment in the back.

I actually have no way of knowing for sure if he has gotten any of my communication, so there really couldn't be any kind of harassment charge.

Charge more for the rent back and have escrow withhold some money as @Andrew Boettcher suggested. 

What rents are they charging?

But they dont tell you that realtors will charge 10k for the 150k house, closing costs, holding costs on the buy and the sell.