After talking with three or four HVAC engineers (who did site visits), we decided to just ditch the HVAC to those two upstairs bedrooms, and install electric heaters in those two rooms.

We're hoping that removing ~10% of the heated square footage from the current furnace doesn't cause us short-cycling issues. However, we may end up replacing the furnace anyways. With all the discounts in place right now, we could do so for ~$1500 - an amount we could make back in ~3 years with the energy savings from the higher efficiency unit.