Circuit for measuring low current output from a high voltage input
The 1nA to 10mA dynamic range, \$10^7\$, that you're asking for is extreme, this would not be possible with a single resistor, so switched resistors would be necessary. An alternative would be to use a silicon diode as the sense element, which would give you log(current), but you would only expect about 10% accuracy, even when using a similar diode run at (say) 100uA as temperature compensation. Maybe that accuracy is all you need?

Having a high side sense and using high voltage high value resistors to bring the differential reading down to ground is a total non-starter. The degree of matching needed to reject the common mode voltage would not be possible.

Two alternatives exist. One is to use low side sensing, interrupting the ground to the load with a sensing element, whether it's a number of switched resistors, or a diode. This may or may not be possible, especially if the load leaks current as corona into the air, not possible to intercept that going to ground. The other is to use high side sensing, in series with the power supply output. 

The trick is to power the sensor, and to get the reading to you. For short runs, using batteries is simple and practical. For indefinite runs, a specially wound transformer should be able to get you 20kV isolation. You could use WiFi (arduino  compatible ESP8266 for instance), or fibre-optics, or a free-space IR LED to a cheap remote control receiver, or even a current to frequency converter driving a loudspeaker with audio!