Regarding the switched tool heads:
I just opened up the Machine Control Panel in Simplify3D for the first time in a long time, and realized that it labels Tool 0 as the right extruder. (Which is what mharter said at the very beginning, I see.) Just ignore what it thinks. T0 is the left extruder.
The official subforum for discussion of the installation and use of the official M2 Dual Extruder upgrade.