Not being familiar with your area’s standard forms I’d say that 99% of the appraisal contingencies I’ve seen either expire automatically (the buyer waives it) or require the buyer to give notice of low appraisal at which point the deal is either renegotiated or cancelled depending on what they say in their notice.

Just off the top of my head.Multifamily---20% down is standard unless it's a you live in FHA, then it's 3.5% down. 

As a standard procedure, we typically do a quiet title action once we take ownership to make sure anyone that might have an interest that was missed gets extinquished. 

Can I tell my tenants:Smoking is not allowed in the house or within a certain distance from entrances(Just like standard rules in offices)All possessions are to be kept inside your unit.

Can anyone help me understand what I should be looking for here, what kind of clauses there should be that are different from a standard operating agreement?

Each municipality has their own zoning and land use regulations and while some are fairly standard, the use of a residential home for short-term rentals is not.

Some units will not meet the standards and it would not make sense to ever rent to sec 8 - for example a basement unit where the ceilings are below 7ft high. 

That's how people get into trouble.Set your standards and stick to them.

I kindly of feel like I’m being played here in the listing agent says that the units are 3/1 when they are 2/1 and creates sqft out of thin air There is no standard on how to measure square footage.

Just use a standard lease and call it a day.