Well, since I didn't get any answers to my questions, I plunged ahead with the install. Hopefully the info below will help someone in a similar situation. I also have a couple remaining HVAC related questions.
Once the TrueZone panel was setup near the furnace and connected to dampers and the 24VAC transformer, I connected my three RC-2000 thermostats using the existing 18-4 thermostat wire to the Zone controller from each location. There was Red (R - power), White (W1 - stage 1 heat), Green (G - fan), and Blue (used for Y - stage 1 cool) on the existing thermostat. I connected the Furnace and AC using the diagram for single stage heat and cool as in the Truezone install guide. With this setup, I was able to run the "Check out" diagnostics on the TrueZone panel and get the furnace to light and the dampers to close and the fan to operate. So the Zone Controller connection to the furnace equipment worked great and operated as expected.
However, I didn't have power to any of the thermostats. I took one of the thermostats downstairs and wired it in right by the panel using a short length of 18-5 wire and connecting the fifth wire to the common, as on p.6 of the RC-2000 install guide, and that powered up the thermostat fine. In addition to another wire for the common, I'll also need a sixth wire if I want to enable the second stage of heat. I'll have to buy some 18-7 wire instead of 18-5 to fish to all three thermostat locations (I haven't seen any other wire options). With our basement renovation, the basement is mostly down to studs so wiring the basement and main floor thermostat location shouldn't be hard, but the 2nd floor thermostat location will take some fishing and drywall repair.
Also, my humidifier is right near the thermostat on the main level, but it runs independently off a separate transformer; it doesn't appear to be connected to the existing thermostat, or furnace fan. I want to connect this to one or all thermostats and remove the old Humidifier control.
Regarding my questions from the post above:
1) I'm using Conventional mode on the Zone Controller for now. With HAI control that I'm after, Conventional mode should be what I need as long as I can eventually do 2 stage heat/1 stage cool.
2) To connect the humidifier, I'm assuming all I have to do is run the additional common leg from the humidifier transformer into the Omnistat 2 common connector, along with the Zone Control common, and then connect the other humidifier wire (Red) to the "Humidifier (H)" connector to control it.
3) Answered this - common wire is required from Zone Control to power Thermostat (also planning to connect humidifier transformer common here)
4) I'm not sure about whether the Omnistat2 can do Two stage heat/Single Stage Cool. It seems the Omnistat 2 can do Single Stage Heat/Cool, and Two stage Heat/Two stage cool, but I'm not sure whether I can/should run this without a second stage AC connection. If the single stage connection shuts off in favor of the second stage connection, then it would seem to shut of my AC right when it's calling for the additional cooling. Another option I see is the Zone Control Mode of the TrueZone controller unit has wiring that connects an additional stage of heat. See p. 7 of the RC-2000 install guide. Or could I possibly bridge the two Cool connections (Y1, Y2) to my single stage AC in Two stage cool mode?
My remaining questions
1) Will the Omnistat 2 thermostats work with Two stage Heat, and single stage cool? If so, what setting/wiring config should I use?
2) Is it advisable to connect the humidifier in parallel to all three thermostats? I'm fishing new wires anyway, and this would seem to allow each zone to include humidification when working independently, which should balance things out more evenly.
3) What gauge of wire to use for the HAI Lumina Pro pabel to Omnistat2 connection? I have a lot of cat 5e around and would prefer to use this to connect thermostats to the HAI panel as I wouldn't have to buy more wire. Is it ok to use this?
Regards,
Choots