They usually already have a listing agreement that stipulates they keep the full 6-7% commission anyway if the buyer doesn’t have an agent, so it’s not always true that you can save 2-3% going directly to the listing agent.

I am assuming you mean you have a loan and there were stipulations about you having to live in the home for a certain amount of time?

I included a stipulation in the contract that seller will convey title via general warranty deed, free of encumbrances.

As for the late rent - be sure you are charging the late fee stipulated in your lease.  

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I had thought of just making a contract and giving him a loan for the amount of my investment with stipulations that we split the profit upon sale or he purchase my interest in the properly if the property isn't sold.

I asked him about this several times and he keeps saying because of all the times I was late, but I've paid late fees, which is the only stipulation in my contract.

Our management agreement stipulates that for major work being done at a property, we do charge 10% of the total.

You have plenty of time to find a new tenant also.... check your local laws - many locations stipulate what you can charge for a lease break. 

He could carry a wrap around mortgage in 2nd position which would give him income over and above the existing debt payment and as part of the deal, he can stipulate a lease to live in the Granny Flat for a set amount of time.