Honeywell TH6320R1004 Wireless Thermostat with Two Transformers
I was able to get the system working by switching the thermostat from 2h/1c Heat Pump mode to 2h/2c Conventional Heat mode. The Honeywell's 2h/1c heat pump mode didn't support 2 transformers (and there wasn't a 2h/1c mode of any sort that did).

I had to swap the Y and the W wires on the thermostat (since it was set up that cool controls O/B which is opposite from conventional heat mode).

My biggest concern now is that the Em-Heat function is not available with this mode but is replaced by Stage 2 Heat and it looks like I can't control when Stage 2 Heat comes on.

With Em-Heat, I had Droop Control and set it to 5 degrees, but this is not an option with Stage 2. I've read that Stage 2 automatically comes on when there is a 2 degree drop, which isn't going to work. So I think I need to spring for a new thermostat. 

The Honeywell THM5421R1021 EIM (using thermostat THX9421 or THM5421R1021) seems to have a heat pump mode supported with two transformers. Anyone have suggestions of a better thermostat solution?