You will want all the points on the schematic labelled “5 V” to actually be 3.3 V, so that the input biassing is correct (i.e. the quiescent input is mid-way between 0 V and 3.3 V, the temperature sensor (if you have one) is OK down to 3.0 V, so the resistors to remove are R7, R9 & R19 and you may or may not need to short out R20, R8 & R18.
If you intend to use the full input range, check the value of burden resistor that you need (as the peak-peak voltage across it needs to be lower). The emonTx uses a 22 Ω burden, so 68 Ω in parallel with the existing burden will be close enough to give you a measuring range on 100 A with our standard CT. (It would have been 66 A maximum without the parallel resistor).
Having now had time to check a schematic and layout of an Arduino Zero, it appears that the Arduino will supply both 5 V and 3.3 V to the Shield, but as you report, it also appears that the Arduino ADC runs on 3.3 V. Therefore, it would seem that you need to cut (or not fit) the 5 V pin on your Shield, and link the track to that pin to the adjacent 3.3 V pin. That will feed all the points labelled 5 V and the points labelled 3.3 V on the Shield with 3.3 V from the Arduino Zero.
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