High voltage, high common mode current measurement. Any suggestions?
The current flowing through the signals your trying to meter doesn't matter in this instance at all, all that matters is the voltage your attempting to measure.  

Any decent voltage metering device will be relatively high impedance (like 10M ohm) the only current that will flow through the meter is a function of the voltage differential being measured between signals and that internal resistance.  The current flowing in the signals being metered doesn't matter at all (other than how it influences the signals voltage).

You are correct that you want to measure differentially, if your meter is earth grounded it most likely needs to withstand the common-mode voltage of the signals.  However its probably easiest just to use a resistor network to divide the voltage down to something safer to plug into your meter.  Again the design of this resistor network doesn't depend on the currents in the signals, just their voltages.  Obviously as this high a voltage you want to use fairly high value resistors.