Well, I think I'll do a compromise solution. I'll shut it all down at
night
when I go to bed. That way, the blower will be off for 4-6 hours.

Why bother? The duty-cycle on most HVAC fans can more than tolerate
constant use. That and the blower fans are relatively inexpensive to
replace should it wear out, say, a year earlier than the 20 years it'll
probably last.

It might be worth having an HVAC professional come out and survey how the
ducting is set up. It's entirely possible that rearranging some ducts might
be in order. Or maybe as simple as better managing the airflow through the
current registers.