You get a 1st lien position on the property, demand note, a JV agreement outlining duties and responsibilities of you and your partner (more his responsibilities to make sure you get paid back), and have him add you as additionally insured on the insurance policy.

Personally, I would contact the seller and renegotiate... your purchase and sale agreement should have outlined that the tenant was occupying the lower unit and that the upper unit was vacant.

Mainly due to the reasons @Josh Key outlined above - Clarksville is heavily dependent on the military base.

@Ryan Murdock True, in your case you outlined from the get go where you are willing to go and what you're willing to do.

If the current owner has a copy of his closing documents, there should be a page that outlines whether or not the lender I going to allow it.

If you have just one it is them and you need to manage them using strategies of the type outlined above.

If so, does the contract or closing documents outline what should take place if/when the 5 year period expires? 

I used generic forms for my first wholesale deal, and ended up with a sharply worded two page long email from the closing attorney outlining everything that was screwed up. 

@Rick Harmon thanks for a clear outline of action!

A scope of work is a document that outlines the specific tasks, deliverables, and milestones that are involved in a project.