Basement has a very large 1000sqft layout that currently has no walls/doors separating rooms, so I'm deciding how I'd convert it to 2 bedrooms with the least amount of construction.

I think more by example so I'll lay out some assumptions first.

John Fedro and I have recently done a webinar about the lay out of the model.  

This is assuming the apartments have decent layouts with decent room sizes.

This is my first post, so I'm going to lay out my whole situation and I'd love some expert insight as to what I should do. 

I usually buy and hold but this property is just an odd layout.

You are looking for similar condition, sold within 6 months, and a similar layout/size. 

I'm late coming to this thread and do not know the floor plan of your duplex, but have you entertained using a ductless split heat pump - one per unit, perhaps with two heads each if warranted by the size and layout.

When I click on the dashboard link the layout is quite a bit different.

Look at the arrangement/layout of the home, particularly the bedroom areas.