My husband is an engineer/ programmer and I'm a financial analyst.

LED light bulbs and a wifi thermostat were the first things we did when moving to our place, not big ticket items, but they more than pay for themselves in time, especially if you leave your lights on for security/aesthetics.

You might check Upwork.com to see about finding a programmer to write a little script to do that.

In order to accomplish this goal, I plan on using my technical skills, critical thinking, and problem solving abilities all of which I have developed as a computer programmer and mathematician.       

If you don't want to go the route of billing by square footage, then there are meters/timers that can be added to the thermostat lines that can record the usage by each unit.

The problem is that there is only one thermostat located in the upper unit.

You can set up stuff to help you manage remotely while you are there such as wireless door locks, ring camera, wifi thermostats, etc..  

Your talking about purchasing all new baseboard units, having them installed, all new electrical wiring run and either a central thermostat or room based thermostats.Regarding your existing furnace, did you only get a parts replacement quote from the one contractor?

On site Wifi controlled or preconfigured keycode devices for thermostats, door locks and the like make management remotely a breeze. 

Reading the story, I'd say what sunk him was changing the locks, removing the thermostat, and removing the mailbox.