For the V5 parts list see
https://community.iotawatt.com/t/building-own-version/1542

For some replacement parts see
https://community.iotawatt.com/t/there-are-no-chips/3469

Tell me about it. For those not familiar with the part numbers, those are the real-time-clock and associated 32.768 crystal.
 They are simply no longer available. I’ve had to find a solution for new units in manufacturing now.

The M41T81 is another i2c SOIC8 clock that is electrically compatible as far as footprint and pinout, and also uses a 32.768 crystal. 
It works pretty much the same as the PCF8523 except that the interface is different.
 IoTaWatt release 02_06_06 recognizes the M41T81 and has been modified to work with it. 
It should also work with the M41T81S which is the latest version. The difference is that the S supports battery-low indication.

For the crystal, there are a few alternatives, especially if you only need a couple.
 It is a 32.768KHZ crystal. Match the specs with another brand: 4-SOJ, 5.50mm pitch, 12.5pF, 50K ohms (although up to 70K should work).

As far as the D1213A-04SO-7 is concerned, those are TVS protection diodes. 
The ADC are good for 5kV, the diodes just take it up to 6 kV to pass some CE tests. For a DIY, you can just leave them off.