If all three of the units are equivalent then 2/3rds of that capital gain would be from investment and 1/3rd from primary residence.The mechanism is that when you sell you will start a 1031 exchange and take boot in the amount equal to the gain attributed to the primary residence portion up to the maximum allowance of $250K ($500K if married).  

You cannot guarantee that the property will appreciate, and if value stays the same, everything is going to be old in 10 years and you'll start to have to spend money to update and replace mechanicals.

One next door neighbor runs a mechanic shop out of his property, the other is vacant and hasn’t been lived in or mowed in at least 5 years.

The mechanics of a personal vs business savings account will be nearly identical meaning they work the same and the interest will be roughly the same. 

And, we are planning on making some significant changes to the mechanicals of the buildings. 

Mechanic.

This would also include mechanics liens, Land Contracts, and anything involving the city/township if there are code violations.

That’s helps me understand the basic mechanics.

A mechanic can fake having credentials and insurance then grossly overcharge you for having for crappy work which you wont know about until things start falling apart.

I doubt many investors ever hit their pro-forma numbers dead-on, there are just too many variables to control when it comes to buildings, mechanical systems, and most of all renters.