My first thought (and test) was to jump the 3 volt and 5 volt pins and cut off the 5 volt pin so the board gets all its feed that way. Problem: boards stacked on top of the driver shield may still be expecting 5 volts to drive displays, etc.
I have a feeling there are going to be a bunch of 3/5 volt challenges ahead, but on the plus side, the Due has capabilities we spent about $20K to get in our lab in 1984!
From Pololu's User Manual on 3V systems:
"Logic power at the same level as your controlling device should be supplied to the VDD pin. This will typically be between 2.5 and 5 V, but the VNH5019 motor drivers are guaranteed to treat any logic input voltage over 2.1 V as high. The only purpose of the VDD pin is to power the pull-up resistors on the EN/DIAG lines."
and
"Current sense output. The pin voltage is roughly 140 mV per amp of output current when the CS_DIS pin is low or disconnected. The current sense reading is more accurate at higher currents. (Note that while the CS voltage can potentially exceed 3 V at high currents, the current sense circuit is safe for use with 3V analog inputs. The MCU’s analog input voltage will be clamped to a safe value by its protection diode, and only a few hundred microamps at most will flow through that diode.)"
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