Power rating of a motor is the mechanical power out.  Divide that by efficiency and you should roughly get electrical power in.  Efficiency will be different if not at full-load.  To get 6W mechanical @ 60% efficiency, you have to put 10W electrical in. 

You have a problem.  Driving motor correctly means generator is going in the incorrect direction, which may explain **But, if I reversed the driving motor supply polarity, the readings stabilized.**  Small, cheap, dc motors can have brushes aligned to get more torque in one direction.

**This simple view assumes I'm getting a nice flat DC waveform out, but I assume it's really like AC straight from a bridge rectifier (don't have a scope) so maybe RMS should come in somewhere?**

Nope.  You have a commutator, which the brushes ride on.  You'd get DC with a ripple.  You could add an inductor in series with output to filter ripple.

On your varying power consumption.  *What size wires and how far is power supply from motor?*  Your efficiency has to be applied to motor and generator.  There is also a mechanical efficiency between the motor and generator.  10W means 6W (60%) from motor and 3.6W (60%) from generator.

Here you also have a problem.  If your generator is at full-load, your motor will be overloaded.  I suggest you graph out input and output (measure voltage and current at different loads).