Adding to the last point, ensure the new debt does not negatively impact your father's DSCR or other financial ratios in a way that might make it harder to secure the next loan.

Sometimes we do that to secure a deal if it's a deal breaker, but we don't typically visit the houses.

My question is, is there anything more I need to do to (i.e. issue a formal written notice of lease violation) in order to prepare for the possibility of keeping a portion of their security deposit to pay for eliminating the odor? 

Consider all the things that could go wrong and see if the lease addresses them: unauthorized pets or tenants, early termination, security deposit, lease violations, late rent, eviction, lawn maintenance, parking, etc.5.

The rate might not be ideal, but securing the property now is crucial—you can always refinance later for better terms.

They often are looking at multiple properties and the more responsive you are, the more likely you will secure the booking.

99.99999% of all lenders are going to come after the secured asset, not the entity's other assets. 

Also check your states Security deposit laws.

Efficient negotiations secured the property for $158,000 on favorable terms.

Finding a property, negotiating a deal, securing a tenant, and managing a rental is seriously hard work!