The other two are 4 units - I can't make the numbers work for just two units unless I'm able to keep the existing unit and add on or construct on the lot. 

It's the single most advantageous regulation in the tax code.  

First question is do they even exist in multi-family and where is the best place to start looking?  

I would require THEM to prove the existence of dangerous mold and that it was your fault, not theirs.

Everyone needs to work together to grow the industry so it becomes more respectable and self-regulated.  

Investing in my backyard is always a better option if the opportunity exists.

Review your contract and scope of work with your subs.Without seeing your contract, I wouldn't know your agreement; but normally, it's always the plumber job to connect water and sewer within your property.The one thing I don't understand is how can the plumber pass inspection, without the inspector look at the connection between the new sewer lateral to the existing line? 

Or option B is to list your property at a price that ought to generate multiple offers that way you can move your your existing property quickly and lock in your up leg property with minimized risk. 

Are there adapters that I could use to attach my new handle to the existing hardware in the shower3.

You don't want the property sitting too long especially given all of the problems that exist which you have no control over (IE location, neighbors, etc).To your success!