That article references California.2nd, I believe it's a misinterpretation of the new California security deposit law which limits security deposits to 1 months rent.

Your goals need to align with whoever your potential investors are.I would schedule a call with a securities attorney, such as @Kim Lisa Taylor to walk through your structure, returns, and business plan, especially if this is your first syndication.There will be demand for your type of deal, especially investors who want a flight to quality in this part of the market cycleGino

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? 

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.

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.

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

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

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

Furthermore, if I am understanding things correctly, RE investors use the equity in their properties to scale/secure more investments, right? 

Also check your states Security deposit laws.