I’ve been in real estate for 10 years, and I’d suggest setting up an Investment LLC for holding properties, a Property Management LLC if you're managing it yourself, and maybe a separate LLC for short-term rentals.

Security deposits require separate handling - they should be placed in an interest-bearing account.3.

If could still do same strategy without it being completely separated.

A Roth IRA is a separate legal entity, different from you. 

The emotional attachment to the idea of paying off my mortgage early still looms large in my brain though.

Selling to someone who loves the home for an emotional reason will get much more money.

Regarding your questions on utilities make sure the multifamily property has separate utilities for each unit.

We are trying to sell two identical buildings separated by an enclosed courtyard.  

We purchased the lot with some friends and completed a CPR and now have 2 separate deeds.

It's great for separating accounts.