I didn't realize the red LED wasn't connected to anything, so I read a little farther and added a wire to link pin 13 and the LED, which snakes neatly between the pin header and the screw terminals.
I plugged it in and started using it with the Data Logger Shield, linking the 3.3 volt supply to the analog reference as suggested (green wire). This led to confusing results as the 3.3 pin was only making intermittent contact with the UNO board due to mechanical interference.
The Dremelled cutout (upper left) clears the USB port on the UNO and doesn't eat any of the proto board holes.
Adafruit recommends trimming the pins on the reset switch (lower left) but there were still clearance problems. I Dremelled the two left most pin joints flush, then cut away a bunch of the plastic from the power connector on the UNO. The package fits together much better now and the 3.3 V signal is reliably there.
Another little detail: The projecting posts from the screw terminals risk shorting to components on the breadboard when used with the Adafruit Experimentation Kit. Cutting them off short seemed like a good pre-emptive strike.