KDR,
That's a big project. I started on zoning 7years ago for a new construction home. After combing through engineering HVAC manuals, software calculators, and rules of thumb for sizing my system - I wound up with 5 different answers. I chickened out and hired a "zoning specialist" to size the furnace, A/C, and ductwork for my house (new construction). I figured I wanted another HVAC "oldtimer", that had already lived though all the wrong answers, to design the system. At least I did install the dampers and zone control components (saved a little dignity).
Your retrofit is a lot tougher. Your system is fully constrained.
I know you're technically oriented, so I apologize in advance if you've already researched the following.
From your description, I gather you are using register dampers. I'm not sure whether the boost fans are register style or inline.
Your major challenge will be to maintain enough air flow across you heat exchanger/A-coil to keep your system from over temping/freezing up the A-coil. If your system over temps your furnace should shut down (you will be taking "life" out of your heat exchanger). Most furnaces do not have sensors on the A-coil. If it freezes, your efficiency will go to nil (it's a block of ice but with far less surface area than your coil). You also run the risk of transferring fluid back to the compressor which will destroy it. Picture cranking over an engine with the cylinders full of water - things will break.
There are two methods for preventing a loss of flow across the A-coil/heat exchanger
- Zone sizing - making sure each zone can support enough flow to keep the system operating efficiently
- Bypassing - installing a bypass duct to shunt flow back into the return side of the furnace
Since you have only one run to the second floor, you will almost certainly need some sort of bypass to keep the airflow constant across your system. This can be simple a simple
adjustable counter weighted damper fed back to the return or a dump zone. You'll need to adjust the counter weight to provide sufficient flow for your minimum system configuration (X dampers closed).
If you have any friends in the business, now is the time to start asking questions.
As I said at the beginning, I'm a EE that has "played" with this (and chickened out). I know just enough to be dangerous.