so you want to home run as many of the 16" supply ducts as possible to the unit itself then? This would require they made the box at the unit (which is another soft box) larger.
I attached a diagram with new Red lines that are changes to the 16" supply lines. Let me know how this looks. When doing this, it dedicates a 16" supply to the problem room side of the house... this would supply more air without changing the ducts I assume (I say this because I don't think those ducts have much of any air flow at this point - not close to the size capacity)
Is it still OK if one of the 16" supply lines comes off the end of the main box, or should they all come off the sides?
Should I keep the existing 18" Return or change it to be 16"?